RunStats.h

#pragma once

#include "include.h"

/**
	RunStats class contains the aggregate statistics for all cohorts run for a given
	input file (simulation context).  Contains all the functions to update these statistics
	and generate the output files.  Its statistics are updated by the StateUpdater objects
	that are called every month for each patient.  Read only access to the
	statistics is provided through accessor functions that return const pointers to the
	subclass objects.
*/
class RunStats
{
public:
	/** Make the StateUpdater class a friend class so it can modify the private data */
	friend class StateUpdater;

	/* Constructors and Destructor */
	RunStats(string runName, SimContext *simContext);
	~RunStats(void);

	/** Constants used for the survival stats groups, excluding top and bottom X percent */
	static const int NUM_SURVIVAL_GROUPS = 4;
	enum SURVIVAL_GROUPS {SURVIVAL_ALL, SURVIVAL_EXCL_LONG, SURVIVAL_EXCL_SHORT, SURVIVAL_EXCL_LONG_AND_SHORT};
	static const int TRUNC_HISTOGRAM_PERC = 5;
	static const int MAX_NUM_HISTOGRAM_BUCKETS = 250;

	/** PatientSummary class holds information that must be stored for every cohort
		even after death, needed to calculate median and other non-incremental statistics */
	class PatientSummary {
	public:
		/** Total costs accrued by the patient */
		double costs;
		/** Total life months lived by the patient */
		double LMs;
		/** Total quality adjusted life months lived by the patient */
		double QALMs;
		/** A struct containing an operator that compares the costs of two summaries that returns true if the first summary had lower costs than the second summary */
		struct compareLMs {
			bool operator()(const PatientSummary &p1, const PatientSummary &p2) const {
				return p1.LMs < p2.LMs;
			}
		};
	}; /* end PatientSummary */

	/** PopulationSummary holds summary aggregate statistics and other misc information */
	class PopulationSummary {
	public:
		// Basic run and set information
		/** The name of the run set this summary belongs to */
		string runSetName;
		/** The name of the run corresponding to this summary */
		string runName;
		/** The date of the run */
		string runDate;
		/** The time the run finished */
		string runTime;
		// Number of patient and clinic visit aggregates
		/** The number of Persons in this cohort */
		int numCohorts;
		/** The number of HIV positive Persons in this cohort */
		int numCohortsHIVPositive;
		/** The total number of clinic visits in this run */
		int totalClinicVisits;
		// Overall costs, life months, and quality adjusted life month statistics
		/** The total cost accrued in this run*/
		double costsSum;
		/** The average costs per Person */
		double costsAverage;
		/** The sum of the squares of the costs per person (for calculating the standard deviation) */
		double costsSumSquares;
		/** The standard deviation of the costs per person */
		double costsStdDev;
		/** The lowest cost per person */
		double costsLowerBound;
		/** The highest cost per person */
		double costsUpperBound;
		/** The total number of life months lived in this run */
		double LMsSum;
		/** The average life months lived per Person */
		double LMsAverage;
		/** The sum of the squares of the life months lived per person (for calculating the standard deviation) */
		double LMsSumSquares;
		/** The standard deviation of the life months lived per person */
		double LMsStdDev;
		/** The lowest life months lived per person */
		double LMsLowerBound;
		/** The highest life months lived per person */
		double LMsUpperBound;
		/** The total number of quality adjusted life months lived in this run */
		double QALMsSum;
		/** The average quality adjusted life months lived per Person */
		double QALMsAverage;
		/** The sum of the squares of the quality adjusted life months lived per person (for calculating the standard deviation) */
		double QALMsSumSquares;
		/** The standard deviation of the quality adjusted life months lived per person */
		double QALMsStdDev;
		/** The lowest quality adjusted life months lived per person */
		double QALMsLowerBound;
		/** The highest quality adjusted life months lived per person */
		double QALMsUpperBound;

		// Overall costs, life months, and quality adjusted life month statistics for use if cohort parsing is turned on
		/** The total cost accrued in this run*/
		double costsSumCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The average costs per Person */
		double costsAverageCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The sum of the squares of the costs per person (for calculating the standard deviation) */
		double costsSumSquaresCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The standard deviation of the costs per person */
		double costsStdDevCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The total number of life months lived in this run */
		double LMsSumCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The average life months lived per Person */
		double LMsAverageCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The sum of the squares of the life months lived per person (for calculating the standard deviation) */
		double LMsSumSquaresCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The standard deviation of the life months lived per person */
		double LMsStdDevCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The total number of quality adjusted life months lived in this run */
		double QALMsSumCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The average quality adjusted life months lived per Person */
		double QALMsAverageCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The sum of the squares of the quality adjusted life months lived per person (for calculating the standard deviation) */
		double QALMsSumSquaresCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];
		/** The standard deviation of the quality adjusted life months lived per person */
		double QALMsStdDevCohortParsing[SimContext::MAX_NUM_SUBCOHORTS];

		/** The average costs per Person using multiple discount rates*/
		double multDiscCostsAverage[SimContext::NUM_DISCOUNT_RATES];
		/** The total costs using multiple discount rates*/
		double multDiscCostsSum[SimContext::NUM_DISCOUNT_RATES];
		/** The sum square costs per Person using multiple discount rates*/
		double multDiscCostsSumSquares[SimContext::NUM_DISCOUNT_RATES];
		/** The standard deviation of the costs per person using multiple discount rates*/
		double multDiscCostsStdDev[SimContext::NUM_DISCOUNT_RATES];
		/** The average LMs per Person using multiple discount rates*/
		double multDiscLMsAverage[SimContext::NUM_DISCOUNT_RATES];
		/** The total LMs per Person using multiple discount rates*/
		double multDiscLMsSum[SimContext::NUM_DISCOUNT_RATES];
		/** The sum square LMs per Person using multiple discount rates*/
		double multDiscLMsSumSquares[SimContext::NUM_DISCOUNT_RATES];
		/** The standard deviation of the LMs per person using multiple discount rates*/
		double multDiscLMsStdDev[SimContext::NUM_DISCOUNT_RATES];
		/** The average QALMs per Person using multiple discount rates*/
		double multDiscQALMsAverage[SimContext::NUM_DISCOUNT_RATES];
		/** The total QALMs per Person using multiple discount rates*/
		double multDiscQALMsSum[SimContext::NUM_DISCOUNT_RATES];
		/** The sum square QALMs per Person using multiple discount rates*/
		double multDiscQALMsSumSquares[SimContext::NUM_DISCOUNT_RATES];
		/** The standard deviation of the QALMs per person using multiple discount rates*/
		double multDiscQALMsStdDev[SimContext::NUM_DISCOUNT_RATES];


		// Aggregate statistics after X number of ART failures
		/** The number of ART failures stratified by ART line */
		int numFailART[SimContext::ART_NUM_LINES+1];
		/** The total costs stratified by most recent ART line failed */
		double costsFailARTSum[SimContext::ART_NUM_LINES+1];
		/** The average cost per person stratified by most recent ART line failed */
		double costsFailARTAverage[SimContext::ART_NUM_LINES+1];
		/** The total life months lived stratified by most recent ART line failed */
		double LMsFailARTSum[SimContext::ART_NUM_LINES+1];
		/** The average life months lived per person stratified by most recent ART line failed */
		double LMsFailARTAverage[SimContext::ART_NUM_LINES+1];
		/** The total quality adjusted life months lived stratified by most recent ART line failed */
		double QALMsFailARTSum[SimContext::ART_NUM_LINES+1];
		/** The average quality adjusted life months lived per person stratified by most recent ART line failed */
		double QALMsFailARTAverage[SimContext::ART_NUM_LINES+1];
		// Overall statistics for HIV positive only
		/** The total costs accrued for HIV positive persons */
		double costsHIVPositiveSum;
		/** The average costs per person accrued for HIV positive persons */
		double costsHIVPositiveAverage;
		/** The total life months lived by HIV positive Persons*/
		double LMsHIVPositiveSum;
		/** The average life months per person lived by HIV positive Persons*/
		double LMsHIVPositiveAverage;
		/** The total quality adjusted life months lived by HIV positive Persons */
		double QALMsHIVPositiveSum;
		/** The average quality adjusted life months per person lived by HIV positive Persons */
		double QALMsHIVPositiveAverage;
	}; /* end PopulationSummary */

	/** HIVScreening holds the statistics related to HIV screening and detection (i.e. the "testing module") */
	class HIVScreening {
	public:
		// number of HIV positive and negative cases
		/** Total number of prevalent HIV cases */
		int numPrevalentCases;
		/** Total number of incident HIV cases */
		int numIncidentCases;
		/** Total number of incident HIV cases by PrEP state */
		int numIncidentCasesByPrEPState[SimContext::HIV_POS_PREP_STATES_NUM];
		/** Total number of HIV negative at initiation */
		int numHIVNegativeAtInit;
		/** Total number of HIV cases */
		int numHIVPositiveTotal;
		/** The number of HIV-negative patients in this cohort who are never infected with HIV, stratified by whether they ever took PrEP */
		int numNeverHIVPositive[SimContext::EVER_PREP_NUM];
		/** The total life months lived by HIV-negative, never infected Persons, stratified by whether they ever took PrEP*/
		double LMsHIVNegativeSum[SimContext::EVER_PREP_NUM];
		/** The average life months per person lived by HIV-negative, never infected Persons, stratified by whether they ever took PrEP*/
		double LMsHIVNegativeAverage[SimContext::EVER_PREP_NUM];
		/** The total quality adjusted life months lived by HIV-negative, never infected Persons, stratified by whether they ever took PrEP*/
		double QALMsHIVNegativeSum[SimContext::EVER_PREP_NUM];
		/** The average quality adjusted life months per person lived by HIV-negative, never infected Persons, stratified by whether they ever took PrEP*/
		double QALMsHIVNegativeAverage[SimContext::EVER_PREP_NUM];
		/** Total number of children whose mother is infected before model start but are themselves uninfected at model start, and total number of children who were ever HIV exposed uninfected after initiation (i.e. were breastfeeding and HIV negative at the time of maternal infection)  */
		int numHIVExposed[3];
		/** Total number of children never exposed to HIV by their mother */
		int numNeverHIVExposed;
		/** Initial counts stratified by HIV state */
		int numPatientsInitialHIVState[SimContext::HIV_EXT_INF_NUM];
		/** Number initially linked to HIV care */
		int numLinkedAtInit[SimContext::HIV_POS_NUM];
		// num prevalent HIV positive patients at detection,
		//	stratified by CD4 x HIV state and HVL x HIV state
		/** Number of prevalent HIV positive patients who become detected */
		int numAtDetectionPrevalent;
		/** Number of prevalent HIV positive patients who become detected stratified by CD4 metric */
		int numAtDetectionPrevalentCD4Metric[SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of prevalent HIV positive patients stratified by HIV state at detection */
		int numAtDetectionPrevalentHIV[SimContext::HIV_POS_NUM];
		/** Number of prevalent HIV positive patients stratified by HIV state at detection and CD4 metric */
		int numAtDetectionPrevalentHIVCD4Metric[SimContext::HIV_POS_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of prevalent HIV positive patients stratified by CD4 strata */
		int numAtDetectionPrevalentCD4[SimContext::CD4_NUM_STRATA];
		/** Number of prevalent HIV positive patients stratified by HIV state at detection and CD4 strata */
		int numAtDetectionPrevalentCD4HIV[SimContext::CD4_NUM_STRATA][SimContext::HIV_POS_NUM];
		/** Number of prevalent HIV positive patients stratified by HVL strata */
		int numAtDetectionPrevalentHVL[SimContext::HVL_NUM_STRATA];
		/** Number of prevalent HIV positive patients stratified by HIV state at detection and HVL strata */
		int numAtDetectionPrevalentHVLHIV[SimContext::HVL_NUM_STRATA][SimContext::HIV_POS_NUM];
		// num incident HIV positive patients at detection,
		//	stratified by CD4 x HIV state and HVL x HIV state
		/** Number of incident HIV positive patients who become detected */
		int numAtDetectionIncident;
		/** Number of incident HIV positive patients who become detected stratified by CD4 metric */
		int numAtDetectionIncidentCD4Metric[SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of incident HIV positive patients stratified by HIV state at detection */
		int numAtDetectionIncidentHIV[SimContext::HIV_POS_NUM];
		/** Number of incident HIV positive patients stratified by HIV state at detection and CD4 metric */
		int numAtDetectionIncidentHIVCD4Metric[SimContext::HIV_POS_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of incident HIV positive patients stratified by CD4 strata */
		int numAtDetectionIncidentCD4[SimContext::CD4_NUM_STRATA];
		/** Percentage of incident HIV positive patients stratified by CD4 strata */
		double percentAtDetectionIncidentCD4[SimContext::CD4_NUM_STRATA];
		/** Number of incident HIV positive patients stratified by HIV state and CD4 strata at detection */
		int numAtDetectionIncidentCD4HIV[SimContext::CD4_NUM_STRATA][SimContext::HIV_POS_NUM];
		/** Number of incident HIV positive patients stratified by HVL strata at detection*/
		int numAtDetectionIncidentHVL[SimContext::HVL_NUM_STRATA];
		/** Percentage of incident HIV positive patients stratified by HVL strata at detection*/
		double percentAtDetectionIncidentHVL[SimContext::HVL_NUM_STRATA];
		/** Number of incident HIV positive patients stratified by HIV state and HVL strata at detection */
		int numAtDetectionIncidentHVLHIV[SimContext::HVL_NUM_STRATA][SimContext::HIV_POS_NUM];
		//num patients at linkage
		//stratified by CD4 x HIV state and HVL x HIV state
		/** Number of HIV positive patients who become linked */
		int numAtLinkage;
		/** Number of HIV positive patients who become linked stratified by CD4 metric*/
		int numAtLinkageCD4Metric[SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of HIV positive patients stratified by HIV state at linkage */
		int numAtLinkageHIV[SimContext::HIV_POS_NUM];
		/** Number of HIV positive patients stratified by HIV state at linkage and CD4 metric*/
		int numAtLinkageHIVCD4Metric[SimContext::HIV_POS_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of HIV positive patients stratified by CD4 strata */
		int numAtLinkageCD4[SimContext::CD4_NUM_STRATA];
		/** Number of HIV positive patients stratified by HVL strata */
		int numAtLinkageHVL[SimContext::HVL_NUM_STRATA];
		/** Number of HIV positive patients stratified by HIV state at linkage and HVL strata */
		int numAtLinkageHVLHIV[SimContext::HVL_NUM_STRATA][SimContext::HIV_POS_NUM];
		/** Number of HIV positive patients stratified by HIV state and CD4 strata at linkage */
		int numAtLinkageCD4HIV[SimContext::CD4_NUM_STRATA][SimContext::HIV_POS_NUM];

		// average CD4 levels at the time of detection (incident and prevalent),
		//	stratified by HIV state
		/** Total CD4 count (prevalent cases) at time of detection */
		double CD4AtDetectionPrevalentSum;
		/** Average CD4 count (prevalent cases) at time of detection */
		double CD4AtDetectionPrevalentAverage;
		/** Total CD4 count (prevalent cases) at time of detection stratified by HIV state at detection - absolute CD4 metric only */
		double CD4AtDetectionPrevalentSumHIV[SimContext::HIV_POS_NUM];
		/** Average CD4 count (prevalent cases) at time of detection stratified by HIV state at detection */
		double CD4AtDetectionPrevalentAverageHIV[SimContext::HIV_POS_NUM];
		/** Total CD4 count (incident cases) at time of detection */
		double CD4AtDetectionIncidentSum;
		/** Average CD4 count (incident cases) at time of detection */
		double CD4AtDetectionIncidentAverage;
		/** Total CD4 count (incident cases) at time of detection stratified by HIV state at detection - absolute CD4 metric only */
		double CD4AtDetectionIncidentSumHIV[SimContext::HIV_POS_NUM];
		/** Average CD4 count (incident cases) at time of detection stratified by HIV state at detection */
		double CD4AtDetectionIncidentAverageHIV[SimContext::HIV_POS_NUM];
		// average CD4 levels at the time of linkage,
		//	stratified by HIV state
		/** Total CD4 count at time of linkage */
		double CD4AtLinkageSum;
		/** Average CD4 count at time of linkage*/
		double CD4AtLinkageAverage;
		/** Total CD4 count at time of linkage stratified by HIV state at linkage - absolute CD4 metric only*/
		double CD4AtLinkageSumHIV[SimContext::HIV_POS_NUM];
		/** Average CD4 count at time of linkage stratified by HIV state at linkage */
		double CD4AtLinkageAverageHIV[SimContext::HIV_POS_NUM];
		// number of months until infection for incident cases
		/** Total number of months until infection for incident cases */
		double monthsToInfectionSum;
		/** Average number of months until infection for incident cases */
		double monthsToInfectionAverage;
		/** Sum of squares of the number of months until infection for incident cases (for calculating standard deviation) */
		double monthsToInfectionSumSquares;
		/** Standard deviation of months until infection for incident cases */
		double monthsToInfectionStdDev;
		// number of months after infection until detection for incident cases
		/** Total number of months after infection until detection for incident cases */
		double monthsAfterInfectionToDetectionSum;
		/** Average number of months after infection until detection for incident cases */
		double monthsAfterInfectionToDetectionAverage;
		/** Sum of squares of the number of months after infection until detection for incident cases */
		double monthsAfterInfectionToDetectionSumSquares;
		/** Standard deviation of the number of months after infection until detection for incident cases */
		double monthsAfterInfectionToDetectionStdDev;
		// number of months to detection for incident and prevalent cases
		/** Total number of months to detection for prevalent cases */
		double monthsToDetectionPrevalentSum;
		/** Average number of months to detection for prevalent cases */
		double monthsToDetectionPrevalentAverage;
		/** Sum of squares of the number of months to detection for prevalent cases (for calculating standard deviation) */
		double monthsToDetectionPrevalentSumSquares;
		/** Standard deviation of the number of months to detection for prevalent cases */
		double monthsToDetectionPrevalentStdDev;
		/** Total number of months to detection for incident cases from model start */
		double monthsToDetectionIncidentSum;
		/** Average number of months to detection for incident cases from model start */
		double monthsToDetectionIncidentAverage;
		/** Sum of squares of the number of months to detection for incident cases from model start (for calculating standard deviation) */
		double monthsToDetectionIncidentSumSquares;
		/** Standard deviation of the number of months to detection for incident cases from model start */
		double monthsToDetectionIncidentStdDev;
		// number of months to linkage
		/** Total number of months to linkage*/
		double monthsToLinkageSum;
		/** Average number of months to linkage*/
		double monthsToLinkageAverage;
		/** Sum of squares of the number of months to linkage (for calculating standard deviation) */
		double monthsToLinkageSumSquares;
		/** Standard deviation of the number of months to linkage */
		double monthsToLinkageStdDev;
		// number of months to linkage stratified by means of detection
		double monthsToLinkageSumMeans[SimContext::HIV_DET_NUM];
		double monthsToLinkageAverageMeans[SimContext::HIV_DET_NUM];
		double monthsToLinkageSumSquaresMeans[SimContext::HIV_DET_NUM];
		double monthsToLinkageStdDevMeans[SimContext::HIV_DET_NUM];

		// age months at time of detection for incident and prevalent cases
		/** Total age months at time of detection for prevalent cases*/
		double ageMonthsAtDetectionPrevalentSum;
		/** Average age months at time of detection for prevalent cases*/
		double ageMonthsAtDetectionPrevalentAverage;
		/** Sum of squares of age months at time of detection for prevalent cases (for calculating standard deviation) */
		double ageMonthsAtDetectionPrevalentSumSquares;
		/** Standard deviation of age months at time of detection for prevalent cases*/
		double ageMonthsAtDetectionPrevalentStdDev;
		/** Total age months at time of detection for incident cases*/
		double ageMonthsAtDetectionIncidentSum;
		/** Average age months at time of detection for incident cases*/
		double ageMonthsAtDetectionIncidentAverage;
		/** Sum of squares of age months at time of detection for incident cases (for calculating standard deviation) */
		double ageMonthsAtDetectionIncidentSumSquares;
		/** Standard deviation of age months at time of detection for incident cases*/
		double ageMonthsAtDetectionIncidentStdDev;
		// age months at time of linkage
		/** Total age months at time of linkage*/
		double ageMonthsAtLinkageSum;
		/** Average age months at time of linkage*/
		double ageMonthsAtLinkageAverage;
		/** Sum of squares of age months at time of linkage (for calculating standard deviation) */
		double ageMonthsAtLinkageSumSquares;
		/** Standard deviation of age months at time of linkage*/
		double ageMonthsAtLinkageStdDev;

		// number patients detected by gender, means of detection, and type of OI presenting
		/** Number of detected patients stratified by gender */
		int numDetectedGender[SimContext::GENDER_NUM];
		/** Number of detected prevalent patients stratified by detection means */
		int numDetectedPrevalentMeans[SimContext::HIV_DET_NUM];
		/** Number of detected incident patients stratified by detection means */
		int numDetectedIncidentMeans[SimContext::HIV_DET_NUM];
		/** Number of linked cases startified by link means*/
		int numLinkedMeans[SimContext::HIV_DET_NUM];
		/** Number of OI detected patients stratified by type of OI leading to detection */
		int numDetectedByOIs[SimContext::OI_NUM];
		/** Number of patients detected by OI who were previously detected by one of the methods, strat by OI */
		int numDetectedByOIsPrevDetected[SimContext::OI_NUM];
		// patient accepting distribution, number that accept and return, and testing intervals
		/** Patient test accepting distribution stratified by HIV status */
		int numTestingAcceptProb[SimContext::TEST_ACCEPT_NUM][SimContext::HIV_EXT_INF_NUM];
		/** Distribution of HIV testing intervals */
		int numTestingInterval[SimContext::HIV_TEST_FREQ_NUM];
		/** Total number of test acceptances */
		int numAcceptTest;
		/** Total number of test refusals */
		int numRefuseTest;
		/** Total number of returns for results */
		int numReturnForResults;
		/** Total number tests where the patient did not return for results*/
		int numNoReturnForResults;

		/** Total number of Lab Staging Accepts */
		int numAcceptLabStaging;
		/** Total number of Lab Staging refusals */
		int numRefuseLabStaging;
		/** Total number of returns for results for Lab Staging*/
		int numReturnForResultsLabStaging;
		/** Total number tests where the patient did not return for results of Lab Staging*/
		int numNoReturnForResultsLabStaging;
		/** Total number of people who link to care through Lab Staging */
		int numLinkLabStaging;
		/** Total number of people who do not link to care through Lab Staging */
		int numNoLinkLabStaging;
		/** Number Accepting Lab Staging stratified by HIV state*/
		int numAcceptLabStagingHIVState[SimContext::HIV_POS_NUM];
		/** Number Returning for results of Lab Staging stratified by HIV state*/
		int numReturnLabStagingHIVState[SimContext::HIV_POS_NUM];
		/** Number of people returning to care through lab staging stratified by Obsv CD4*/
		int numReturnLabStagingObsvCD4[SimContext::CD4_NUM_STRATA];
		/** Number of people returning to care through lab staging stratified by True CD4*/
		int numReturnLabStagingTrueCD4[SimContext::CD4_NUM_STRATA];
		/** Number of people returning through lab staging stratified by Observed and True CD4*/
		int numReturnLabStagingObsvTrueCD4[SimContext::CD4_NUM_STRATA][SimContext::CD4_NUM_STRATA];
		/** Number of people linking to care through lab staging stratified by Obsv CD4*/
		int numLinkLabStagingObsvCD4[SimContext::CD4_NUM_STRATA];
		/** Number of people linking to care through lab staging stratified by True CD4*/
		int numLinkLabStagingTrueCD4[SimContext::CD4_NUM_STRATA];
		/** Number of people linking through lab staging stratified by Observed and True CD4*/
		int numLinkLabStagingObsvTrueCD4[SimContext::CD4_NUM_STRATA][SimContext::CD4_NUM_STRATA];

		// number of tests performed and number of each result
		/** Number of HIV tests given stratified by HIV state */
		int numTestsHIVState[SimContext::HIV_EXT_INF_NUM];
		/** Number of Test results given to prevalent patients */
		int numTestResultsPrevalent;
		/** Number of Test results given to prevalent patients stratified by test result */
		int numTestResultsPrevalentType[SimContext::TEST_RESULT_NUM];
		/** Number of Test results given to incident patients */
		int numTestResultsIncident;
		/** Number of Test results given to incident patients stratified by test result */
		int numTestResultsIncidentType[SimContext::TEST_RESULT_NUM];
		/** Number of Test results given to HIV negative patients */
		int numTestResultsHIVNegative;
		/** Number of Test results given to HIV negative patients stratified by test result */
		int numTestResultsHIVNegativeType[SimContext::TEST_RESULT_NUM];

		// Number of patients who ever take PrEP
		int numEverPrEP;
		// Number of patients who drop out of PrEP
		int numDropoutPrEP;
		// Number of patients who stop PrEP due to screening age limit
		int numStopPrEPMaxAge;

		//EID
		/** number of EID test results stratified by type of test*/
		int numEIDTestsGivenType[SimContext::EID_TEST_TYPE_NUM];
		int numTruePositiveEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];
		int numTrueNegativeEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];
		int numFalsePositiveEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];
		int numFalseNegativeEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];

		/** Total number of EID test results stratified by test num*/
		int numEIDTestsGivenTest[SimContext::EID_NUM_TESTS];
		/** Total number of true positive EID test results by test num */
		int numTruePositiveEIDTestResultsTest[SimContext::EID_NUM_TESTS];
		/** Total number of true negative EID test results by test num */
		int numTrueNegativeEIDTestResultsTest[SimContext::EID_NUM_TESTS];
		/** Total number of false positive EID test results by test num */
		int numFalsePositiveEIDTestResultsTest[SimContext::EID_NUM_TESTS];
		/** Total number of false negative EID test results by test num */
		int numFalseNegativeEIDTestResultsTest[SimContext::EID_NUM_TESTS];

		/** Number of months spent false positive*/
		double LMsFalsePositive;
		double LMsFalsePositiveLinked;
	};

	/** SurvivalStats holds total survival statistics, used with different survival
		group types that exclude X percent bottom and top survival numbers */
	class SurvivalStats {
	public:
		/** Histogram of life months survival */
		map<int,int> LMsHistogram;
		// Aggregate life months statistics
		/** Minimum number of life months lived */
		double LMsMin;
		/** Maximum number of life months lived */
		double LMsMax;
		/** Median number of life months lived */
		double LMsMedian;
		/** Sum deviation from median number of life months lived */
		double LMsSumDeviationMedian;
		/** Average deviation from median number of life months lived */
		double LMsAverageDeviationMedian;
		/** Total number of life months lived */
		double LMsSum;
		/** Average number of life months lived */
		double LMsMean;
		/** Sum Deviation of the number of life months lived */
		double LMsSumDeviation;
		/** Average Deviation of the number of life months lived */
		double LMsAverageDeviation;
		/** Sum Deviation Squares of the number of life months lived */
		double LMsSumDeviationSquares;
		/** Standard Deviation of the number of life months lived */
		double LMsStdDev;
		/** Variance of the number of life months lived */
		double LMsVariance;
		/** Sum Deviation Cubes of the number of life months lived */
		double LMsSumDeviationCubes;
		/** Skew of the number of life months lived */
		double LMsSkew;
		/** Sum Deviation Quads of the number of life months lived */
		double LMsSumDeviationQuads;
		/** Kurtosis of the number of life months lived */
		double LMsKurtosis;
		// Costs and quality adjusted life months statistics
		/** Total costs accrued */
		double costsSum;
		/** Total costs accrued per person */
		double costsMean;
		/** Sum of squares of costs accrued */
		double costsSumSquares;
		/** Standard deviation of costs accrued */
		double costsStdDev;
		/** Total quality adjusted life months lived */
		double QALMsSum;
		/** Average quality adjusted life months lived */
		double QALMsMean;
		/** Sum of squares of quality adjusted life months lived */
		double QALMsSumSquares;
		/** Standard deviation of quality adjusted life months lived */
		double QALMsStdDev;
	}; /* end SurvivalStats */

	/** InitialDistributions class contains statistics about the initial patient state */
	class InitialDistributions {
	public:
		// CD4 and HVL histograms
		/** Histogram of initial CD4 stratas */
		int numPatientsCD4Level[SimContext::CD4_NUM_STRATA];
		/** Histogram of initial HVL stratas */
		int numPatientsHVLLevel[SimContext::HVL_NUM_STRATA];
		/** Histogram of initial setpoint levels */
		int numPatientsHVLSetpointLevel[SimContext::HVL_NUM_STRATA];
		// Age and gender statistics
		/** Total initial age (in months) - HIV+ only; if a patient starts HIV-negative their age at time of infection is added */
		double sumInitialAgeMonths;
		/** Average initial age in months - HIV+ only; if they start the model HIV-negative this is their age at the time of infection */
		double averageInitialAgeMonths;
		/** Total number of male patients */
		int numMalePatients;
		/** Total number of female patients */
		int numFemalePatients;
		/** Prior OI history statistics */
		int numPriorOIHistories[SimContext::OI_NUM];
		/** ART response type for CD4 effects */
		int numARTResposneTypes[SimContext::CD4_RESPONSE_NUM_TYPES];
		/** Prevalent generic risk factors */
		int numRiskFactors[SimContext::RISK_FACT_NUM];
		/** Pediatrics HIV and maternal state */
		int numInitialPediatrics[SimContext::PEDS_HIV_NUM][SimContext::PEDS_MATERNAL_STATUS_NUM];
	}; /* end InitialDistributions */

	/** CHRMsStats class contains aggregates and distributions of CHRMs occurrences  (CHRM = chronic-hepatic-renal-malignancies) */
	class CHRMsStats {
	public:
		/** The number of people that had a CHRM stratified by CHRM */
		int numPatientsWithCHRM[SimContext::CHRM_NUM];
		/** The number of HIV+ people that had a CHRM stratified by CHRM */
		int numPatientsWithCHRMHIVPos[SimContext::CHRM_NUM];
		/** The number of HIV- people that had a CHRM stratified by CHRM */
		int numPatientsWithCHRMHIVNeg[SimContext::CHRM_NUM];
		/** The number of HIV+ patients with prevalent CHRMs stratified by CHRM */
		int numPrevalentCHRM[SimContext::CHRM_NUM];
		/** The number of HIV- patients with prevalent CHRMs stratified by CHRM */
		int numPrevalentCHRMHIVNeg[SimContext::CHRM_NUM];
		/** The total number of HIV-negative people that had a prevalent CHRM */
		int numHIVNegWithPrevalentCHRMs;

		/** The number of prevalent CHRMs stratified by CD4 */
		int numPrevalentCD4[SimContext::CD4_NUM_STRATA];
		/** The number of prevalent CHRMs stratified by both CHRM and CD4 */
		int numPrevalentCHRMCD4[SimContext::CHRM_NUM][SimContext::CD4_NUM_STRATA];
		/** The number of incident CHRMs in HIV+ patients stratified by CHRM */
		int numIncidentCHRM[SimContext::CHRM_NUM];
		/** The number of incident CHRMs in HIV- patients stratified by CHRM */
		int numIncidentCHRMHIVneg[SimContext::CHRM_NUM];
		/** The total number of HIV-negative people that had an incident CHRM */
		int numHIVNegWithIncidentCHRMs;

		/** The number of incident CHRMs stratified by CD4 */
		int numIncidentCD4[SimContext::CD4_NUM_STRATA];
		/** The number of incident CHRMs stratified by both CHRM and CD4 */
		int numIncidentCHRMCD4[SimContext::CHRM_NUM][SimContext::CD4_NUM_STRATA];
		/** The number of CHRM related deaths in HIV+ patients stratified by CHRM */
		int numDeathsCHRM[SimContext::CHRM_NUM];
		/** The number of CHRM related deaths stratified by CD4 */
		int numDeathsCD4[SimContext::CD4_NUM_STRATA];
		/** The number of CHRM related deaths stratified by both CHRM and CD4 */
		int numDeathsCHRMCD4[SimContext::CHRM_NUM][SimContext::CD4_NUM_STRATA];
	};

	/** OIStats class contains aggregates and distributions of OI occurrences */
	class OIStats {
	public:
		// Primary, secondary and detected OI counts,
		//	stratified by OI type, CD4 level, and OI type x CD4 level
		/** Primary OI count stratified by OI type */
		int numPrimaryOIsOI[SimContext::OI_NUM];
		/** Primary OI count stratified by CD4 strata */
		int numPrimaryOIsCD4[SimContext::CD4_NUM_STRATA];
		/** Primary OI count stratified by OI type and CD4 strata */
		int numPrimaryOIsCD4OI[SimContext::CD4_NUM_STRATA][SimContext::OI_NUM];
		/** Secondary OI count stratified by OI type */
		int numSecondaryOIsOI[SimContext::OI_NUM];
		/** Secondary OI count stratified by CD4 strata */
		int numSecondaryOIsCD4[SimContext::CD4_NUM_STRATA];
		/** Secondary OI count stratified by OI type and CD4 strata */
		int numSecondaryOIsCD4OI[SimContext::CD4_NUM_STRATA][SimContext::OI_NUM];
		/** Detected OI count stratified by OI type */
		int numDetectedOIsOI[SimContext::OI_NUM];
		/** Detected OI count stratified by CD4 strata */
		int numDetectedOIsCD4[SimContext::CD4_NUM_STRATA];
		/** Detected OI count stratified by OI type and CD4 strata */
		int numDetectedOIsCD4OI[SimContext::CD4_NUM_STRATA][SimContext::OI_NUM];
		/** Total OI events across the whole run */
		int numOIEventsTotal;
		// OI history logging - number of patients and calculated probabilities of having OI history
		//	stratified by OI x HVL, OI x CD4, and OI x HVL x CD4
		/** Total number of patients stratified by viral load (used for calculating averages) */
		int numPatientsHVL[SimContext::HVL_NUM_STRATA];
		/** Total number of patients stratified by CD4 strata (used for calculating averages) */
		int numPatientsCD4[SimContext::CD4_NUM_STRATA];
		/** Total number of patients stratified by viral load and CD4 strata (used for calculating averages) */
		int numPatientsHVLCD4[SimContext::HVL_NUM_STRATA][SimContext::CD4_NUM_STRATA];
		/** Total number of patients with a history of each OI type stratified by viral load (used for calculating averages) */
		int numPatientsOIHistoryHVL[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA];
		/** Total number of patients with a history of each OI type stratified by CD4 count (used for calculating averages) */
		int numPatientsOIHistoryCD4[SimContext::OI_NUM][SimContext::CD4_NUM_STRATA];
		/** Total number of patients with a history of each OI type stratified by viral load and CD4 count (used for calculating averages) */
		int numPatientsOIHistoryHVLCD4[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA][SimContext::CD4_NUM_STRATA];
		/** Proportion of patients with a history of each OI stratified by viral load */
		double probPatientsOIHistoryHVL[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA];
		/** Proportion of patients with a history of each OI stratified by CD4 strata */
		double probPatientsOIHistoryCD4[SimContext::OI_NUM][SimContext::CD4_NUM_STRATA];
		/** Proportion of patients with a history of each OI stratified by viral load and CD4 strata */
		double probPatientsOIHistoryHVLCD4[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA][SimContext::CD4_NUM_STRATA];
		/** Number of months spent at each viral load strata (used for calculating averages) */
		int numMonthsHVL[SimContext::HVL_NUM_STRATA];
		/** Number of months spent at each CD4 strata (used for calculating averages) */
		int numMonthsCD4[SimContext::CD4_NUM_STRATA];
		/** Number of months spent at each viral load and CD4 strata combination (used for calculating averages) */
		int numMonthsHVLCD4[SimContext::HVL_NUM_STRATA][SimContext::CD4_NUM_STRATA];
		/** Number of months spent at each viral load strata with a history of each OI */
		int numMonthsOIHistoryHVL[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA];
		/** Number of months spent at each CD4 strata with a history of each OI */
		int numMonthsOIHistoryCD4[SimContext::OI_NUM][SimContext::CD4_NUM_STRATA];
		/** Number of months spent at each viral load strata and CD4 strata combination with a history of each OI */
		int numMonthsOIHistoryHVLCD4[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA][SimContext::CD4_NUM_STRATA];
		/** Calculated proportion of months spent with a history of OI in each viral load strata*/
		double probMonthsOIHistoryHVL[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA];
		/** Calculated proportion of months spent with a history of OI in each CD4 strata*/
		double probMonthsOIHistoryCD4[SimContext::OI_NUM][SimContext::CD4_NUM_STRATA];
		/** Calculated proportion of months spent with a history of OI in each viral load and CD4 strata combination */
		double probMonthsOIHistoryHVLCD4[SimContext::OI_NUM][SimContext::HVL_NUM_STRATA][SimContext::CD4_NUM_STRATA];
	}; /* end OIStats */

	/** DeathStats contains the statistics and distributions of causes of deaths */
	class DeathStats {
	public:
		// Number of deaths stratified by Cause, CD4, and Cause x CD4
		/** Number of deaths in HIV+ patients stratified by death cause */
		int numDeathsHIVPosType[SimContext::DTH_NUM_CAUSES];
		/** Number of deaths in all patients stratified by death cause */
		int numDeathsType[SimContext::DTH_NUM_CAUSES];
        /** Number of deaths stratified by type and age */
		int numDeathsTypeAge[SimContext::DTH_NUM_CAUSES][SimContext::OUTPUT_AGE_CAT_NUM];
		/** Number of deaths stratified by CD4 strata */
		int numDeathsCD4[SimContext::CD4_NUM_STRATA];
		/** Number of deaths stratified by death cause and CD4 strata */
		int numDeathsCD4Type[SimContext::CD4_NUM_STRATA][SimContext::DTH_NUM_CAUSES];
		/** Number of deaths stratified by care status */
		int numDeathsCare[SimContext::HIV_CARE_NUM];
		/** Number of deaths stratified by death cause and care status */
		int numDeathsCareType[SimContext::HIV_CARE_NUM][SimContext::DTH_NUM_CAUSES];

		/** Total Number of deaths due to ART Tox*/
		int numARTToxDeaths;
		/** Number of deaths due to ART Tox stratified by age category for cd4 metric*/
		int numARTToxDeathsCD4Metric[SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of deaths due to ART Tox stratified by cd4*/
		int numARTToxDeathsCD4[SimContext::CD4_NUM_STRATA];
		/** Number of deaths due to ART Tox stratified by cd4 and hvl*/
		int numARTToxDeathsCD4HVL[SimContext::CD4_NUM_STRATA][SimContext::HVL_NUM_STRATA];
		/** Number of deaths due to ART Tox stratified by CD4 HVL and OI Hist*/
		int numARTToxDeathsCD4HVLOIHist[SimContext::CD4_NUM_STRATA][SimContext::HVL_NUM_STRATA][SimContext::OI_NUM];
		/** probability of having oi history for those who died from ART tox stratified by cd4 and hvl and OI */
		double probOIHistARTToxDeathsCD4HVL[SimContext::CD4_NUM_STRATA][SimContext::HVL_NUM_STRATA][SimContext::OI_NUM];
		/** distribution of people who died from tox based on cd4 and hvl*/
		double hvlDistribToxDeathCD4HVL[SimContext::CD4_NUM_STRATA][SimContext::HVL_NUM_STRATA];

		/** Number of HIV negative deaths */
		int numDeathsUninfected;
		/** Number of deaths stratified by HVL and CD4 combination */
		int numDeathsHVLCD4[SimContext::HVL_NUM_STRATA][SimContext::CD4_NUM_STRATA];
		/** Number of deaths stratified by HVL */
		int numDeathsHVL[SimContext::HVL_NUM_STRATA];
		// Number of HIV and background mortality deaths stratified by CD4 and OI history
		/** Number of HIV deaths with no OI history */
		int numHIVDeathsNoOIHistory;
		/** Number of HIV deaths with no OI history stratified by CD4 strata */
		int numHIVDeathsNoOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Number of HIV deaths with OI history */
		int numHIVDeathsOIHistory;
		/** Number of HIV deaths with OI history stratified by CD4 strata */
		int numHIVDeathsOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Number of background mortality deaths with no OI history */
		int numBackgroundMortDeathsNoOIHistory;
		/** Number of background mortality deaths with no OI history stratified by CD4 strata */
		int numBackgroundMortDeathsNoOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Number of background mortality deaths with OI history */
		int numBackgroundMortDeathsOIHistory;
		/** Number of background mortality deaths with OI history stratified by CD4 strata */
		int numBackgroundMortDeathsOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Sum of CD4's of all patients who died from art Tox*/
		double ARTToxDeathsCD4Sum;
		/** Sum of Squares of CD4's of all patients who died from Tox*/
		double ARTToxDeathsCD4SumSquares;
		/** mean CD4 of all patients who died from art Tox*/
		double ARTToxDeathsCD4Mean;
		/** std dev CD4 of all patients who died from art Tox*/
		double ARTToxDeathsCD4StdDev;

	}; /* end DeathStats */

	/** OverallSurvival stats contains aggregate survival statistics, separate from
		SurvivalSummary since these will only be calculated for all cohorts and not subset groups */
	class OverallSurvival {
	public:
		// life months without OI history, with OI history, and both
		//	stratified by totals and CD4
		/** Total life months lived without OI history by HIV+ patients*/
		double LMsNoOIHistory;
		/** Total life months lived without OI history by HIV+ patients stratified by CD4 strata */
		double LMsNoOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Total life months lived with OI history */
		double LMsOIHistory;
		/** Total life months lived with OI history stratified by CD4 strata */
		double LMsOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Total life months lived by HIV+ patients*/
		double LMsTotal;
		/** Total life months lived stratified by CD4 strata */
		double LMsTotalCD4[SimContext::CD4_NUM_STRATA];
		// life months stratified by HVL and HVL setpoint
		/** Total life months lived stratified by HVL strata */
		double LMsHVL[SimContext::HVL_NUM_STRATA];
		/** Total life months lived stratified by setpoint HVL strata */
		double LMsHVLSetpoint[SimContext::HVL_NUM_STRATA];
		// life months with and without OI history, stratified by OI type
		/** Total life months lived without OI history stratified by OI type */
		double LMsNoOIHistoryOIs[SimContext::OI_NUM];
		/** Total life months lived with OI history stratified by OI type */
		double LMsOIHistoryOIs[SimContext::OI_NUM];
		/** Total life months lived with CHRM History for HIV+ patients stratified by CHRM type */
		double LMsCHRMHistoryCHRMsHIVPos[SimContext::CHRM_NUM];
		/** Total life months lived with CHRM History for HIV- patients stratified by CHRM type */
		double LMsCHRMHistoryCHRMsHIVNeg[SimContext::CHRM_NUM];
		// life months stratified by HIV state and HIV positive total
		/** Total life months lived with HIV */
		double LMsHIVPositive;
		/** Total life months lived in each HIV state */
		double LMsHIVState[SimContext::HIV_ID_NUM];
		/** Total quality adjusted life months lived with HIV */
		double QALMsHIVPositive;
		/** Total quality adjusted life months lived in each HIV state */
		double QALMsHIVState[SimContext::HIV_ID_NUM];
		// life months in screening state and regular model
		/** Total life months lived in the screening state */
		double LMsInScreening;
		/** Total quality adjusted life months lived in the screening state */
		double QALMsInScreening;
		// Total life months lived by HIV-negative patients on PrEP
		double LMsHIVNegativeOnPrEP;
		/** Total life months lived in "regular CEPAC" (i.e. non-screening state) */
		double LMsInRegularCEPAC;
		
		// life months by gender
		/** Total life months lived stratified by gender */
		double LMsGender[SimContext::GENDER_NUM];
		/** Total quality adjusted life months lived stratified by gender */
		double QALMsGender[SimContext::GENDER_NUM];
	}; /* end OverallSurvival */

	/** OverallCosts class contains aggregate cost stats */
	class OverallCosts {
	public:
		// costs without OI history, with OI history, and both
		//	stratified by totals and CD4
		/** Total costs accrued without OI history */
		double costsNoOIHistory;
		/** Total costs accrued without OI history stratified by CD4 */
		double costsNoOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Total costs accrued with OI history */
		double costsOIHistory;
		/** Total costs accrued with OI history stratified by CD4 */
		double costsOIHistoryCD4[SimContext::CD4_NUM_STRATA];
		/** Total costs accrued */
		double costsTotal;
		/** Total costs accrued stratified by CD4 */
		double costsTotalCD4[SimContext::CD4_NUM_STRATA];
		// costs stratified by HVL and HVL setpoint
		/** Total costs accrued stratified by HVL */
		double costsHVL[SimContext::HVL_NUM_STRATA];
		/** Total costs accrued stratified by HVL setpoint */
		double costsHVLSetpoint[SimContext::HVL_NUM_STRATA];
		// direct medical costs for prophylaxis, stratified by total, OI, and OI x proph line
		/** Total direct medical costs for prophylaxis */
		double directCostsProph;
		/** Direct medical costs for prophylaxis stratified by OI type */
		double directCostsProphOIs[SimContext::OI_NUM];
		/** Direct medical costs for prophylaxis stratified by OI type and prophylaxis line */
		double directCostsProphOIsProph[SimContext::OI_NUM][SimContext::PROPH_NUM];
		// direct costs for ART, stratified by total and ART line
		/** Direct costs for ART */
		double directCostsART;
		/** Direct costs for ART stratified by ART line*/
		double directCostsARTLine[SimContext::ART_NUM_LINES];
		/** Direct costs for ART if using mult discount rates*/
		double directCostsARTMultDisc[SimContext::NUM_DISCOUNT_RATES];
		double directCostsARTLineMultDisc[SimContext::ART_NUM_LINES][SimContext::NUM_DISCOUNT_RATES];
		/**Costs for initiating a line of art*/
		double costsARTInit;
		/**Costs for initiating a line of art by art line*/
		double costsARTInitLine[SimContext::ART_NUM_LINES];
		/**Monthly costs of art*/
		double costsARTMonthly;
		/**Monthly costs of art by art line*/
		double costsARTMonthlyLine[SimContext::ART_NUM_LINES];
		/** monthly and init costs for art if using  multiple discount rates*/
		double costsARTInitMultDisc[SimContext::NUM_DISCOUNT_RATES];
		double costsARTInitLineMultDisc[SimContext::ART_NUM_LINES][SimContext::NUM_DISCOUNT_RATES];
		double costsARTMonthlyMultDisc[SimContext::NUM_DISCOUNT_RATES];
		double costsARTMonthlyLineMultDisc[SimContext::ART_NUM_LINES][SimContext::NUM_DISCOUNT_RATES];

		// costs stratified by HIV states and total for HIV positives
		/** Total costs for HIV positive patients */
		double costsHIVPositive;
		/** Total costs stratified by HIV states */
		double costsHIVState[SimContext::HIV_ID_NUM];
		// costs for various screening and testing
		/** Total costs for CD4 tests */
		double costsCD4Testing;
		/** Total costs for HVL tests */
		double costsHVLTesting;
		/** costs of cd4 and hvl testing for multiple discount rates*/
		double costsCD4TestingMultDisc[SimContext::NUM_DISCOUNT_RATES];
		double costsHVLTestingMultDisc[SimContext::NUM_DISCOUNT_RATES];

		/** Total TB costs (Discounted)*/
		double costsTBTotal;
		/** Costs of TB tests */
		double costsTBTests;
		double costsTBTestsInit[SimContext::TB_NUM_TESTS];
		double costsTBTestsDST[SimContext::TB_NUM_TESTS];
		/** costs of TB treatment */
		double costsTBTreatment;
		double costsTBTreatmentByLine[SimContext::TB_NUM_TREATMENTS];
		double costsTBTreatmentToxByLine[SimContext::TB_NUM_TREATMENTS];
		/** TB Visit Costs */
		double costsTBProviderVisits[SimContext::COST_NUM_TYPES];
		double costsTBMedicationVisits[SimContext::COST_NUM_TYPES];

		/** Total costs for clinic visits */
		double costsClinicVisits;
		/** Total PrEP costs */
		double costsPrEP;
		/** Total PrEP costs for those never infected with HIV */
		double costsPrEPNeverHIV;
		/** Total PrEP costs for those who have had PrEP but get HIV by PrEP status*/
		double costsPrEPHIVPos[SimContext::HIV_POS_PREP_STATES_NUM-1];
		/** Total costs for HIV screening tests */
		double costsHIVScreeningTests;
		/** Total costs for HIV screening miscellaneous costs */
		double costsHIVScreeningMisc;
		/** Total Costs for Lab Staging tests */
		double costsLabStagingTests;
		/** Total Costs for EID tests */
		double costsEIDTests;
		/** Total costs for Lab Staging misc costs*/
		double costsLabStagingMisc;
		/** Total Costs for EID misc costs */
		double costsEIDMisc;
		/** Total costs for EID visits */
		double costsEIDVisits;
		/** Total costs for Infant HIV Proph */
		double costsInfantHIVProph;
		// undiscounted costs stratified by cost type and unclassified costs
		/** Total undiscounted costs stratified by cost type */
		double totalUndiscountedCosts[SimContext::COST_NUM_TYPES];
		/** Total undiscounted unclassified costs */
		double totalUndiscountedCostsUnclassified;
		// discounted costs stratified by cost type and unclassified costs
		/** Total discounted costs stratified by cost type */
		double totalDiscountedCosts[SimContext::COST_NUM_TYPES];
		/** Total discounted unclassified costs */
		double totalDiscountedCostsUnclassified;
		// costs for drugs and toxicities
		/** Costs due to drugs */
		double costsDrugs;
		double costsDrugsDiscounted;
		/**costs due to adherence interventions*/
		double costsInterventionStartup;
		double costsInterventionMonthly;
		/** Costs due to toxicity*/
		double costsToxicity;
		double costsToxicityDiscounted;
		/** Costs due to CHRMs*/
		double costsCHRMs[SimContext::CHRM_NUM];
		/** Total costs stratified by gender */
		double costsGender[SimContext::GENDER_NUM];

	}; /* end OverallCosts */

	/** TBStats class contains stats about TB occurrences, treatments, and costs */
	class TBStats {
	public:
		/** Total number with TB disease at model entry for those infected with TB, stratified by TB strain x TB state */
		int numInStateAtEntryStrain[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_STATES];
		/** Total number uninfected with TB at model entry*/
		int numUninfectedTBAtEntry;
		/** Total number with each combination of unfavorable outcomes */
		int numWithUnfavorableOutcome[2][2][2][2];

		// number with various TB treatment effects, stratified by TB strain x TB treatment number
		/** Total number of times patients start a TB treatment regimen stratified by observed TB strain x TB treatment number */
		int numStartOnTreatment[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_TREATMENTS];
		/** Total number who drop out of TB treatment stratified by observed TB strain x TB treatment number */
		int numDropoutTreatment[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_TREATMENTS];
		/** Total number who transition to TB Treatment Default state (i.e. are cured of TB despite dropping out of treatment) stratified by observed TB strain x TB treatment number */
		int numTransitionsToTBTreatmentDefault[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_TREATMENTS];
		/** Total number of times patients finish treatment stratified by observed TB strain x TB treatment number */
		int numFinishTreatment[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_TREATMENTS];
		/** Total number who are cured after finishing treatment stratified by true TB strain x TB treatment number */
		int numCuredAtTreatmentFinish[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_TREATMENTS];
		/** Total number with increased resistance after stopping treatment stratified by true TB strain before increase x TB treatment number - XDR is included in declaration for convenience but should never be incremented or output*/
		int numIncreaseResistanceAtTreatmentStop[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_TREATMENTS];
		// total number of infections and reinfections, stratified by TB strain and TB state
		int numInfections[SimContext::TB_NUM_STATES][SimContext::TB_NUM_STRAINS];
		/** Total number of reactivations from latent TB stratified by TB strain */
		int numReactivationsLatent[SimContext::TB_NUM_STRAINS];
		int numReactivationsPulmLatent[SimContext::TB_NUM_STRAINS];
		int numReactivationsExtraPulmLatent[SimContext::TB_NUM_STRAINS];

		// number of relapses from treated or default TB states, stratified by TB strain
		int numRelapses[SimContext::TB_NUM_STRAINS];
		int numRelapsesPulm[SimContext::TB_NUM_STRAINS];
		int numRelapsesExtraPulm[SimContext::TB_NUM_STRAINS];

		/** Total number of self-cures from active TB, stratified by TB strain */
		int numTBSelfCures[SimContext::TB_NUM_STRAINS];
		/** Total number of deaths from active TB, stratified by TB strain */
		int numDeaths[SimContext::TB_NUM_STRAINS];
		// Total number of deaths from active TB in HIV-positive patients, stratified by TB strain
		int numDeathsHIVPos[SimContext::TB_NUM_STRAINS];
		// Total number of deaths from active TB in HIV-negative patients, stratified by TB strain
		int numDeathsHIVNeg[SimContext::TB_NUM_STRAINS];
		/** Total number of minor toxicities stratified by treatment line */
		int numTreatmentMinorToxicity[SimContext::TB_NUM_TREATMENTS];
		/** Total number of major toxicities stratified by treatment line */
		int numTreatmentMajorToxicity[SimContext::TB_NUM_TREATMENTS];
		/** Total number of minor toxicities stratified by proph line */
		int numProphMinorToxicity[SimContext::TB_NUM_PROPHS];
		/** Total number of major toxicities stratified by proph line */
		int numProphMajorToxicity[SimContext::TB_NUM_PROPHS];
		// Number of DST test results for those without Tb by observed strain
		int numDSTTestResultsUninfectedTB[SimContext::TB_NUM_STRAINS];
		// Number of DST test results for those by observed strain and true strain [obsv][true]
		int numDSTTestResultsByTrueTBStrain[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_STRAINS];

	}; /* end TBStats */

	/** LTFUStats contains stats about patient loss to follow up and return to care */
	class LTFUStats {
	public:
		// totals for patients that were ever lost and deaths while lost
		/** Total number of patients ever lost*/
		int numPatientsLost;
		/** Total number of patients who ever returned */
		int numPatientsReturned;
		/** Total number of deaths occurring while lost from care */
		int numDeathsWhileLost;
		// totals for times ltfu and rtc stratified by CD4
		/** Total number of LTFU occurrences */
		int numLostToFollowUp;
		/** Total number of LTFU occurrences stratified by CD4*/
		int numLostToFollowUpCD4[SimContext::CD4_NUM_STRATA];
		/** Total number of RTC occurrences */
		int numReturnToCare;
		/** Total number of RTC occurrences stratified by CD4*/
		int numReturnToCareCD4[SimContext::CD4_NUM_STRATA];
		/** Total number of deaths occurring while lost from care stratified by CD4*/
		int numDeathsWhileLostCD4[SimContext::CD4_NUM_STRATA];
		// time lost before returning to care
		/** Total time lost before returning to care */
		double monthsLostBeforeReturnSum;
		/** Average time lost before returning to care per patient*/
		double monthsLostBeforeReturnMean;
		/** Sum of squares of total time lost before returning to care (for calculating standard deviation) */
		double monthsLostBeforeReturnSumSquares;
		/** Standard deviation of time lost before returning to care per patient*/
		double monthsLostBeforeReturnStdDev;
		// number lost to follow up during ART line or pre/post ART
		/** Number lost to follow up while on each ART line */
		int numLostToFollowUpART[SimContext::ART_NUM_LINES];
		/** Number lost to follow up pre-ART */
		int numLostToFollowUpPreART;
		/** Number lost to follow up post-ART */
		int numLostToFollowUpPostART;
		// number return to care on prev ART line or subsequent ART line
		/** Number who returned to care and started previous ART line */
		int numReturnOnPrevART[SimContext::ART_NUM_LINES];
		/** Number who returned to care and started the next ART line */
		int numReturnOnNextART[SimContext::ART_NUM_LINES];
		/** Number who returned to care pre-ART */
		int numReturnToCarePreART;
		/** Number who returned to care post-ART */
		int numReturnToCarePostART;
		// number of deaths while lost by prev ART line
		/** Number of deaths while lost stratified by most recent ART line taken */
		int numDeathsWhileLostART[SimContext::ART_NUM_LINES];
		/** Number of deaths while lost pre-ART */
		int numDeathsWhileLostPreART;
		/** Number of deaths while lost post-ART */
		int numDeathsWhileLostPostART;
	};

	/** ProphStats class contains statistics about prophylaxis treatments and toxicities */
	class ProphStats {
	public:
		// number of toxicities stratified by OI type and OI type x proph line
		/** Number of minor toxicities stratified by OI type and prophylaxis line */
		int numMinorToxicity[SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** Number of minor toxicities stratified by OI type */
		int numMinorToxicityTotal[SimContext::OI_NUM];
		/** Number of major toxicities stratified by OI type and prophylaxis line */
		int numMajorToxicity[SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** Number of major toxicities stratified by OI type */
		int numMajorToxicityTotal[SimContext::OI_NUM];
		// average true CD4, observed CD4, and times prophylaxis initiated for primary and
		//	secondary OIs, stratified by OI type x proph line
		/** Total true CD4 initiated for primary and secondary OIs, stratified by OI type and proph line*/
		double trueCD4InitProphSum[SimContext::PROPH_NUM_TYPES][SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** Average true CD4 initiated for primary and secondary OIs, stratified by OI type and proph line*/
		double trueCD4InitProphMean[SimContext::PROPH_NUM_TYPES][SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** Total observed CD4 initiated for primary and secondary OIs, stratified by OI type and proph line*/
		double observedCD4InitProphSum[SimContext::PROPH_NUM_TYPES][SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** Average observed CD4 initiated for primary and secondary OIs, stratified by OI type and proph line*/
		double observedCD4InitProphMean[SimContext::PROPH_NUM_TYPES][SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** Total number of times primary and secondary prophylaxis was started, stratified by OI type and proph line*/
		int numTimesInitProph[SimContext::PROPH_NUM_TYPES][SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** Total number of times primary and secondary prophylaxis was started, stratified by OI type, proph line and CD4 metric*/
		int numTimesInitProphCD4Metric[SimContext::PROPH_NUM_TYPES][SimContext::OI_NUM][SimContext::PROPH_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total number of times primary and secondary prophylaxis was started by patients with an observed CD4 (Absolute CD4 metric only), stratified by OI type and proph line*/
		int numTimesInitProphWithObservedCD4[SimContext::PROPH_NUM_TYPES][SimContext::OI_NUM][SimContext::PROPH_NUM];
	}; /* end ProphStats */

	/**  ARTStats contains stats about ART treatments and toxicities */
	class ARTStats {
	public:
		// months in suppressed state, stratified by total and ART line
		/** Total months in suppressed state */
		int monthsSuppressed;
		/** Total months in suppressed state, stratified by ART line */
		int monthsSuppressedLine[SimContext::ART_NUM_LINES];
		/** Total months in failed state stratified by ART line */
		int monthsFailedLine[SimContext::ART_NUM_LINES];
		/** Total months in failed state stratified by HVL */
		int monthsFailedHVL[SimContext::HVL_NUM_STRATA];
		/** Total months in failed state stratified by ART line and HVL */
		int monthsFailedLineHVL[SimContext::ART_NUM_LINES][SimContext::HVL_NUM_STRATA];
		// statistics at ART initiation, stratified by ART line x response type
		/** Total number initiating ART stratified by ART line */
		int numOnARTAtInit[SimContext::ART_NUM_LINES];
		/** Total number initiating ART stratified by ART line and CD4 metric */
		int numOnARTAtInitCD4Metric[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total number with absolute CD4 metric initiating ART stratified by ART line, and response type - currently unused output, should be double checked before use; may need to add another output to accommodate Peds < 5 and CD4 percent metric */
		int numOnARTAtInitResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Total true CD4 counts at ART initialization stratified by ART line and CD4 metric */
		double trueCD4AtInitSum[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 counts at ART initialization stratified by ART line and CD4 metric */
		double trueCD4AtInitMean[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 counts at ART initialization stratified by ART line,hetergeneity outcomes, and response type */
		double trueCD4AtInitSumResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Average true CD4 counts at ART initialization stratified by ART line and response type - currently unused output, should be double checked before use*/
		double trueCD4AtInitMeanResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Total number initiating ART with observed CD4 (Absolute CD4 metric only) stratified by ART line, and response type - currently unused output, should be double checked before use */
		int numWithObservedCD4AtInitResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Total observed CD4 counts at ART initialization stratified by ART line */
		double observedCD4AtInitSum[SimContext::ART_NUM_LINES];
		/** Number of patients with observed CD4 (absolute CD4 metric) at ART initialization stratified by ART line */
		int numWithObservedCD4AtInit[SimContext::ART_NUM_LINES];
		/** Average observed CD4 counts at ART initialization stratified by ART line */
		double observedCD4AtInitMean[SimContext::ART_NUM_LINES];
		/** Total observed CD4 counts at ART initialization stratified by ART line and response type */
		double observedCD4AtInitSumResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Average observed CD4 counts at ART initialization stratified by ART line and response type */
		double observedCD4AtInitMeanResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Histogram of ART efficacies drawn at ART initialization stratified by ART line and efficacy type */
		int numDrawEfficacyAtInit[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		/** Histogram of ART efficacies drawn at ART initialization stratified by ART line and efficacy type and response type - currently unused output, should be double checked before use */
		int numDrawEfficacyAtInitResp[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Histogram of CD4 response type drawn at ART initialization stratified by ART line and CD4 response type */
		int numCD4ResponseTypeAtInit[SimContext::ART_NUM_LINES][SimContext::CD4_RESPONSE_NUM_TYPES];
		/** Histogram of CD4 response type drawn at ART initialization stratified by ART line and CD4 response type  and ART response type - currently unused output, should be double checked before use */
		int numCD4ResponseTypeAtInitResp[SimContext::ART_NUM_LINES][SimContext::CD4_RESPONSE_NUM_TYPES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Histogram of risk factors at ART initialization stratified by ART line and risk factor */
		int numWithRiskFactorAtInit[SimContext::ART_NUM_LINES][SimContext::RISK_FACT_NUM];
		/** Histogram of risk factors at ART initialization stratified by ART line and risk factor and ART response type - currently unused output, should be double checked before use */
		int numWithRiskFactorAtInitResp[SimContext::ART_NUM_LINES][SimContext::RISK_FACT_NUM][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		// statistics at ART true failure, stratified by ART line x response type
		/** Number of ART true failure, stratified by ART line */
		int numTrueFailure[SimContext::ART_NUM_LINES];
		/** Number of ART true failure, stratified by ART line and CD4 metric*/
		int numTrueFailureCD4Metric[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Number of ART true failure in those with absolute CD4 metric, stratified by ART line x response type */
		int numTrueFailureResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Total true CD4 at true failure stratified by ART line and CD4 metric*/
		double trueCD4AtTrueFailureSum[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at true failure stratified by ART line and CD4 metric*/
		double trueCD4AtTrueFailureMean[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 (Absolute CD4 metric only) at true failure stratified by ART line x response type */
		double trueCD4AtTrueFailureSumResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Average true CD4 at true failure stratified by ART line x response type */
		double trueCD4AtTrueFailureMeanResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Total observed CD4 at true failure stratified by ART line */
		double observedCD4AtTrueFailureSum[SimContext::ART_NUM_LINES];
		/** Number of patients with observed CD4 (Absolute Metric Only) at true failure stratified by ART line */
		int numWithObservedCD4AtTrueFailure[SimContext::ART_NUM_LINES];
		/** Average observed CD4 at true failure stratified by ART line */
		double observedCD4AtTrueFailureMean[SimContext::ART_NUM_LINES];
		/** Total observed CD4 at true failure stratified by ART line x response type */
		double observedCD4AtTrueFailureSumResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Number of patients with observed CD4 (Absolute Metric Only) at true failure stratified by ART line x response type */
		int numWithObservedCD4AtTrueFailureResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Average observed CD4 at true failure stratified by ART line x response type */
		double observedCD4AtTrueFailureMeanResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Total months to true failure stratified by ART line */
		double monthsToTrueFailureSum[SimContext::ART_NUM_LINES];
		/** Average months to true failure stratified by ART line */
		double monthsToTrueFailureMean[SimContext::ART_NUM_LINES];
		/** Total months to true failure stratified by ART line and response type */
		double monthsToTrueFailureSumResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Average months to true failure stratified by ART line and response type */
		double monthsToTrueFailureMeanResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Sum of squares of months to true failure stratified by ART line (used to calculate standard deviation) */
		double monthsToTrueFailureSumSquares[SimContext::ART_NUM_LINES];
		/** Standard deviation of months to true failure stratified by ART line */
		double monthsToTrueFailureStdDev[SimContext::ART_NUM_LINES];
		/** Sum of squares of months to true failure stratified by ART line and response type (used to calculate standard deviation) */
		double monthsToTrueFailureSumSquaresResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		/** Standard deviation of months to true failure stratified by ART line and response type */
		double monthsToTrueFailureStdDevResp[SimContext::ART_NUM_LINES][SimContext::HET_NUM_OUTCOMES][SimContext::RESP_NUM_TYPES];
		// total number and true/observed CD4 at observed failure,
		//	stratified by ART line and ART line x failure type
		/** Total number of observed failures stratified by ART line */
		int numObservedFailure[SimContext::ART_NUM_LINES];
		/** Total number of observed failures stratified by ART line and CD4 metric */
		int numObservedFailureCD4Metric[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total number of observed failures stratified by ART line and failure type */
		int numObservedFailureType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		/** Total number of observed failures stratified by ART line, failure type, and CD4 metric */
		int numObservedFailureTypeCD4Metric[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total number of observed failures after true failure stratified by ART line */
		int numObservedFailureAfterTrue[SimContext::ART_NUM_LINES];
		/** Total number of observed failures after true failure stratified by ART line and failure type */
		int numObservedFailureAfterTrueType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		/** Total number never observed to fail stratified by ART line */
		int numNeverObservedFailure[SimContext::ART_NUM_LINES];
		/** Total true CD4 at observed failure stratified by ART line and CD4 metric */
		double trueCD4AtObservedFailureSum[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at observed failure stratified by ART line and CD4 metric */
		double trueCD4AtObservedFailureMean[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 at observed failure stratified by ART line, failure type and CD4 metric*/
		double trueCD4AtObservedFailureSumType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at observed failure stratified by ART line, failure type and CD4 metric */
		double trueCD4AtObservedFailureMeanType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES][SimContext::PEDS_CD4_AGE_CAT_NUM];

		/** Total number of patients with observed CD4 (Absolute CD4 metric only) at observed failure stratified by ART line */
		int numObservedCD4atObservedFailure[SimContext::ART_NUM_LINES];
		/** Total observed CD4 at observed failure stratified by ART line */
		double observedCD4AtObservedFailureSum[SimContext::ART_NUM_LINES];
		/** Average observed CD4 at observed failure stratified by ART line */
		double observedCD4AtObservedFailureMean[SimContext::ART_NUM_LINES];
		/** Total number of patients with observed CD4 (Absolute CD4 metric only) at observed failure stratified by ART line and failure type */
		int numObservedCD4atObservedFailureType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		/** Total observed CD4 at observed failure stratified by ART line and failure type */
		double observedCD4AtObservedFailureSumType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		/** Average observed CD4 at observed failure stratified by ART line and failure type */
		double observedCD4AtObservedFailureMeanType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		// average and std dev of number of months between true failure and observed failure,
		//	stratified by ART line and ART line x failure type
		/** Total months to observed failure stratified by ART line */
		double monthsToObservedFailureSum[SimContext::ART_NUM_LINES];
		/** Average months to observed failure stratified by ART line */
		double monthsToObservedFailureMean[SimContext::ART_NUM_LINES];
		/** Total months to observed failure stratified by ART line and failure type */
		double monthsToObservedFailureSumType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		/** Average months to observed failure stratified by ART line and failure type */
		double monthsToObservedFailureMeanType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		/** Total sum of squares of months to observed failure stratified by ART line (used for calculating standard deviation) */
		double monthsToObservedFailureSumSquares[SimContext::ART_NUM_LINES];
		/** Standard deviation of months to observed failure stratified by ART line */
		double monthsToObservedFailureStdDev[SimContext::ART_NUM_LINES];
		/** Total sum of squares of months to observed failure stratified by ART line and failure type (used for calculating standard deviation) */
		double monthsToObservedFailureSumSquaresType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		/** Standard deviation of months to observed failure stratified by ART line and failure type */
		double monthsToObservedFailureStdDevType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_FAIL_TYPES];
		// number who stop ART and true/observed CD4, stratified by ART line and ART line x stop type
		/** Total number who stop ART stratified by ART line*/
		int numStop[SimContext::ART_NUM_LINES];
		/** Total number who stop ART stratified by ART line and CD4 metric*/
		int numStopCD4Metric[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total number who stop ART stratified by ART line x stop type */
		int numStopType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		/** Total number who stop ART stratified by ART line x stop type and CD4 metric*/
		int numStopTypeCD4Metric[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total number who stop ART after true failure stratified by ART line */
		int numStopAfterTrueFailure[SimContext::ART_NUM_LINES];
		/** Total number who stop ART after true failure stratified by ART line x stop type */
		int numStopAfterTrueFailureType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		/** Total number who never stop ART stratified by ART line*/
		int numNeverStop[SimContext::ART_NUM_LINES];
		/** Total true CD4 at ART stop, stratified by ART line and CD4 metric*/
		double trueCD4AtStopSum[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at ART stop, stratified by ART line and CD4 metric*/
		double trueCD4AtStopMean[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 at ART stop, stratified by ART line x stop type and CD4 metric*/
		double trueCD4AtStopSumType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at ART stop, stratified by ART line x stop type and CD4 metric*/
		double trueCD4AtStopMeanType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total number with observed CD4 (Absolute CD4 metric only) at ART stop stratified by ART line*/
		int numWithObservedCD4Stop[SimContext::ART_NUM_LINES];
		/** Total number with observed CD4 (Absolute CD4 metric only) at ART stop stratified by ART line x stop type */
		int numWithObservedCD4StopType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];		
		/** Total observed CD4 at ART stop, stratified by ART line */
		double observedCD4AtStopSum[SimContext::ART_NUM_LINES];
		/** Average observed CD4 at ART stop, stratified by ART line */
		double observedCD4AtStopMean[SimContext::ART_NUM_LINES];
		/** Total observed CD4 at ART stop, stratified by ART line x stop type*/
		double observedCD4AtStopSumType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		/** Average observed CD4 at ART stop, stratified by ART line x stop type*/
		double observedCD4AtStopMeanType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		// months on art before stopping, stratified by ART line and ART line x stop type
		/** Total months on art before stopping, stratified by ART line */
		double monthsToStopSum[SimContext::ART_NUM_LINES];
		/** Average months on art before stopping, stratified by ART line */
		double monthsToStopMean[SimContext::ART_NUM_LINES];
		/** Total months on art before stopping, stratified by ART line x stop type */
		double monthsToStopSumType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		/** Average months on art before stopping, stratified by ART line x stop type */
		double monthsToStopMeanType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		/** Sum of squares of months on art before stopping, stratified by ART line (for calculating standard deviation) */
		double monthsToStopSumSquares[SimContext::ART_NUM_LINES];
		/** Standard deviation of months on art before stopping, stratified by ART line */
		double monthsToStopStdDev[SimContext::ART_NUM_LINES];
		/** Sum of squares of months on art before stopping, stratified by ART line x stop type (for calculating standard deviation) */
		double monthsToStopSumSquaresType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		/** Standard deviation of months on art before stopping, stratified by ART line x stop type */
		double monthsToStopStdDevType[SimContext::ART_NUM_LINES][SimContext::ART_NUM_STOP_TYPES];
		//number of deaths while on ART line
		/** num deaths on ART*/
		int numARTDeath[SimContext::ART_NUM_LINES];
		/** num deaths on ART stratified by ART line and CD4 metric*/
		int numARTDeathCD4Metric[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 at death on ART, stratified by ART line and CD4 metric */
		double trueCD4AtARTDeathSum[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at death on ART, stratified by ART line and CD4 metric */
		double trueCD4AtARTDeathMean[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total observed CD4 at death on ART, stratified by ART line */
		double observedCD4AtARTDeathSum[SimContext::ART_NUM_LINES];
		/** Number of HIV+ patients with observed CD4 at death on ART, stratified by ART line */
		int numWithObservedCD4AtARTDeath[SimContext::ART_NUM_LINES];
		/** Average observed CD4 death on ART, stratified by ART line */
		double observedCD4AtARTDeathMean[SimContext::ART_NUM_LINES];
		/** Total propensity at death on ART, stratified by ART line */
		double propensityAtARTDeathSum[SimContext::ART_NUM_LINES];
		/** Average propensity at death on ART, stratified by ART line */
		double propensityAtARTDeathMean[SimContext::ART_NUM_LINES];
		/** num deaths on ART*/
		int numARTDeathCause[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES];
		/** num deaths on ART stratified by CD4 metric*/
		int numARTDeathCauseCD4Metric[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 at death on ART, stratified by ART line, cause of death and CD4 metric */
		double trueCD4AtARTDeathCauseSum[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at death on ART, stratified by ART line, cause of death and CD4 metric */
		double trueCD4AtARTDeathCauseMean[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total observed CD4 at death on ART, stratified by ART line and cause of death*/
		double observedCD4AtARTDeathCauseSum[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES];
		/** Number of HIV+ patients with observed CD4 at death on ART, stratified by ART line and cause of death*/
		int numWithObservedCD4AtARTDeathCause[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES];
		/** Average observed CD4 death on ART, stratified by ART line and cause of death*/
		double observedCD4AtARTDeathCauseMean[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES];
		/** Total propensity at death on ART, stratified by ART line and cause of death*/
		double propensityAtARTDeathCauseSum[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES];
		/** Average propensity at death on ART, stratified by ART line and cause of death*/
		double propensityAtARTDeathCauseMean[SimContext::ART_NUM_LINES][SimContext::DTH_NUM_CAUSES];

		/** num OIs on ART by ART line and OI type*/
		int numARTOI[SimContext::ART_NUM_LINES][SimContext::OI_NUM];
		/** num OIs on ART stratified by ART line, OI type and CD4 metric*/
		int numARTOICD4Metric[SimContext::ART_NUM_LINES][SimContext::OI_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 at OI on ART, stratified by ART line, OI and CD4 metric*/
		double trueCD4AtARTOISum[SimContext::ART_NUM_LINES][SimContext::OI_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at OI on ART, stratified by ART line, OI and CD4 metric*/
		double trueCD4AtARTOIMean[SimContext::ART_NUM_LINES][SimContext::OI_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total observed CD4 at oi on ART, stratified by ART line and OI*/
		double observedCD4AtARTOISum[SimContext::ART_NUM_LINES][SimContext::OI_NUM];
		/** Number of HIV+ patients with observed CD4 at OI on ART, stratified by ART line and OI type*/
		int numWithObservedCD4AtARTOI[SimContext::ART_NUM_LINES][SimContext::OI_NUM];
		/** Average observed CD4 oi on ART, stratified by ART line and OI*/
		double observedCD4AtARTOIMean[SimContext::ART_NUM_LINES][SimContext::OI_NUM];
		/** Total propensity at oi on ART, stratified by ART line and OI*/
		double propensityAtARTOISum[SimContext::ART_NUM_LINES][SimContext::OI_NUM];
		/** Average propensity at oi on ART, stratified by ART line and OI*/
		double propensityAtARTOIMean[SimContext::ART_NUM_LINES][SimContext::OI_NUM];

		/** num people who ever Ever Initiated ART line*/
		int numARTEverInit[SimContext::ART_NUM_LINES];
		/** num people who ever Ever Initiated each ART line stratified by CD4 measurement age category */
		int numARTEverInitCD4Metric[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total true CD4 at ART EverInit first time regimen, stratified by ART line and CD4 metric*/
		double trueCD4AtARTEverInitSum[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Average true CD4 at EverInit first time regimen, stratified by ART line and CD4 metric */
		double trueCD4AtARTEverInitMean[SimContext::ART_NUM_LINES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** Total observed CD4 at  EverInit first time regimen, stratified by ART line*/
		double observedCD4AtARTEverInitSum[SimContext::ART_NUM_LINES];
		/** Number of HIV+ patients with observed CD4 at EverInit first time regimen, stratified by ART line*/
		int numWithObservedCD4AtARTEverInit[SimContext::ART_NUM_LINES];
		/** Average observed CD4 EverInit first time regimen, stratified by ART line*/
		double observedCD4AtARTEverInitMean[SimContext::ART_NUM_LINES];
		/** Total propensity at EverInit first time regimen, stratified by ART line*/
		double propensityAtARTEverInitSum[SimContext::ART_NUM_LINES];
		/** Average propensity at EverInit first time regimen, stratified by ART line*/
		double propensityAtARTEverInitMean[SimContext::ART_NUM_LINES];

		// number on ART, number suppressed, and HVL drop at specified month time points,
		//	stratified by ART line x month to record
		/** Number on ART stratified by ART line and month to record */
		unsigned int numOnARTAtMonth[SimContext::ART_NUM_LINES][SimContext::ART_NUM_MTHS_RECORD];
		/** Number suppressed on ART stratified by ART line and month to record */
		unsigned int numSuppressedAtMonth[SimContext::ART_NUM_LINES][SimContext::ART_NUM_MTHS_RECORD];
		/** Total number of HVL drops stratified by ART line and month to record */
		double HVLDropsAtMonthSum[SimContext::ART_NUM_LINES][SimContext::ART_NUM_MTHS_RECORD];
		/** Average number of HVL drops stratified by ART line and month to record */
		double HVLDropsAtMonthMean[SimContext::ART_NUM_LINES][SimContext::ART_NUM_MTHS_RECORD];
		/** Sum of squares of HVL drops stratified by ART line and month to record (for calculating standard deviation) */
		double HVLDropsAtMonthSumSquares[SimContext::ART_NUM_LINES][SimContext::ART_NUM_MTHS_RECORD];
		/** Standard deviation of HVL drops stratified by ART line and month to record */
		double HVLDropsAtMonthStdDev[SimContext::ART_NUM_LINES][SimContext::ART_NUM_MTHS_RECORD];
		/** Distribution at ART initiation, stratified by ART line x CD4 x HVL */
		int distributionAtInit[SimContext::ART_NUM_LINES][SimContext::CD4_NUM_STRATA][SimContext::HVL_NUM_STRATA];
		/** number of toxicity cases, stratified by ART line x tox severity x HVL */
		int numToxicityCases[SimContext::ART_NUM_LINES][SimContext::ART_NUM_TOX_SEVERITY][SimContext::HVL_NUM_STRATA];
		/** number of toxicity deaths, stratified by ART line x HVL */
		int numToxicityDeaths[SimContext::ART_NUM_LINES][SimContext::HVL_NUM_STRATA];
		// number of STI interruptions, restarts, endpoints, and patients with interruptions,
		//	stratified by ART line x STI cycle
		/** Total number of STI interruptions, stratified by ART line x STI cycle */
		int numSTIInterruptions[SimContext::ART_NUM_LINES][SimContext::STI_NUM_TRACKED];
		/** Total number of STI restarts, stratified by ART line x STI cycle */
		int numSTIRestarts[SimContext::ART_NUM_LINES][SimContext::STI_NUM_TRACKED];
		/** Total number of STI endpoints, stratified by ART line x STI cycle */
		int numSTIEndpoints[SimContext::ART_NUM_LINES][SimContext::STI_NUM_TRACKED];
		/** Total number of patients with interruptions, stratified by ART line x STI cycle - currently appears redundant and identical to numSTIInterruptions*/
		int numPatientsWithSTIInterruptions[SimContext::ART_NUM_LINES][SimContext::STI_NUM_TRACKED];
		// number and duartion of STI interruptions, stratified by ART line
		/** Total number of STI interruptions stratified by ART line */
		double numSTIInterruptionsSum[SimContext::ART_NUM_LINES];
		/** Average number of STI interruptions stratified by ART line */
		double numSTIInterruptionsMean[SimContext::ART_NUM_LINES];
		/** Total duration of STI interruptions stratified by ART line */
		double monthsOnSTIInterruptionSum[SimContext::ART_NUM_LINES];
		/** Average duration of STI interruptions stratified by ART line */
		double monthsOnSTIInterruptionMean[SimContext::ART_NUM_LINES];
	}; /* end ARTStats */

	/** TimeSummary class contains monthly/yearly longitudinal stats */
	class TimeSummary {
	public:
		/** Time period month or year */
		int timePeriod;
		/** number alive at this time*/
		int numAlive;
		/** number alive stratified by TB status */
		int numAliveTB[SimContext::TB_NUM_STATES];
		/** number alive with TB tracker stratified by hiv status */
		int numAliveTBTrackerCare[SimContext::TB_NUM_TRACKER][SimContext::HIV_CARE_NUM];
		/** number LTFU from TB care */
		int numTBLTFU;
		/** number on TB Proph this month by proph line and true TB state */
		int numOnTBProph[SimContext::TB_NUM_PROPHS][SimContext::TB_NUM_STATES];
		/** number who completed the full duration on each TB Proph line this month by true TB state */
		int numCompletedTBProph[SimContext::TB_NUM_PROPHS][SimContext::TB_NUM_STATES];
		/** number of times drug resistance increased for people in active states on each TB proph line stratified by true TB strain before the increase - XDR is included in declaration for convenience but should never be incremented or output*/
		int numIncreaseResistanceDueToProph[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_PROPHS];
		/** number who had minor toxicity on each TB proph line this month */
		int numTBProphMinorTox[SimContext::TB_NUM_PROPHS];
		/** number who had major toxicity on each TB proph line this month */
		int numTBProphMajorTox[SimContext::TB_NUM_PROPHS];
		/** number on TB Treatment by true TB state and treat line*/
		int numOnTBTreatmentByState[SimContext::TB_NUM_STATES][SimContext::TB_NUM_TREATMENTS];
		/** number on Empiric Tb Treatment by true TB state and treat line*/
		int numOnEmpiricTBTreatmentByState[SimContext::TB_NUM_STATES][SimContext::TB_NUM_TREATMENTS];
		/** number on TB Treatment by treat line*/
		int numOnTBTreatmentTotal[SimContext::TB_NUM_TREATMENTS];
		/** number on Empiric Tb Treatment by treat line*/
		int numOnEmpiricTBTreatmentTotal[SimContext::TB_NUM_TREATMENTS];
		/** number infected with TB stratified by TB Strain*/
		int numTBStrain[SimContext::TB_NUM_STRAINS];
		/** number hiv + with TB tracker stratified by tracker and cd4 */
		int numHIVTBTrackerCD4[SimContext::TB_NUM_TRACKER][SimContext::CD4_NUM_STRATA];
		// total number of infections and reinfections this time period, stratified by TB state and TB drug resistance strain
		int numTBInfections[SimContext::TB_NUM_STATES][SimContext::TB_NUM_STRAINS];
		/** number of reactivations from latent TB this time period, stratified by TB strain*/
		int numTBReactivationsLatent[SimContext::TB_NUM_STRAINS];
		int numTBReactivationsPulmLatentHIVNegative[SimContext::TB_NUM_STRAINS];
		int numTBReactivationsExtraPulmLatentHIVNegative[SimContext::TB_NUM_STRAINS];
		int numTBReactivationsPulmLatentHIVPositive[SimContext::CD4_NUM_STRATA][SimContext::TB_NUM_STRAINS];
		int numTBReactivationsExtraPulmLatentHIVPositive[SimContext::CD4_NUM_STRATA][SimContext::TB_NUM_STRAINS];
		// number of relapses from treated or default TB states, stratified by TB strain
		int numTBRelapses[SimContext::TB_NUM_STRAINS];
		int numTBRelapsesPulm[SimContext::TB_NUM_STRAINS];
		int numTBRelapsesExtraPulm[SimContext::TB_NUM_STRAINS];
		//number with observed tb
		int numObservedTBUninfectedTB[SimContext::TB_NUM_STRAINS];
		//number with observed tb stratified by true tb status [obsv][true]
		int numObservedTBByTrueTBStrain[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_STRAINS];
		// Number of TB test results by Test num, TB state, and result
		int numTBTestResults[SimContext::TB_NUM_TESTS][SimContext::TB_NUM_STATES][SimContext::TB_DIAG_STATUS_NUM];
		// Number of final TB diagnostic chain results by TB state and result
		int numTBDiagnosticResults[SimContext::TB_NUM_STATES][SimContext::TB_DIAG_STATUS_NUM];
		// Number of DST test results for those without Tb by observed strain
		int numDSTTestResultsUninfectedTB[SimContext::TB_NUM_STRAINS];
		// Number of DST test results for those by observed strain and true strain [obsv][true]
		int numDSTTestResultsByTrueTBStrain[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_STRAINS];

		// Number alive with unfavorabe TB outcome */
		int numTBUnfavorableOutcome[2][2][2][2];
		// Number deaths with unfavorable outcome */
		int numDeathsTBUnfavorableOutcome[2][2][2][2];


		//number on succesful tb treatment(real and empiric) stratified by Treatment line
		int numOnSuccessfulTBTreatment[SimContext::TB_NUM_TREATMENTS];
		int numOnSuccessfulTBTreatmentPulm[SimContext::TB_NUM_TREATMENTS];
		int numOnSuccessfulTBTreatmentExtraPulm[SimContext::TB_NUM_TREATMENTS];
		//number on failed tb treatment(real and empiric) stratified by Treatment line
		int numOnFailedTBTreatment[SimContext::TB_NUM_TREATMENTS];
		int numOnFailedTBTreatmentPulm[SimContext::TB_NUM_TREATMENTS];
		int numOnFailedTBTreatmentExtraPulm[SimContext::TB_NUM_TREATMENTS];
		//number that default on tb treatment stratified by Treatment line
		int numDefaultTBTreatment[SimContext::TB_NUM_TREATMENTS];
		int numDefaultTBTreatmentPulm[SimContext::TB_NUM_TREATMENTS];
		int numDefaultTBTreatmentExtraPulm[SimContext::TB_NUM_TREATMENTS];
		// number who drop out of TB treatment this time period stratified by observed TB strain x TB treatment line
		int numDropoutTBTreatment[SimContext::TB_NUM_STRAINS][SimContext::TB_NUM_TREATMENTS];

		//TB Deaths
		int numDeathsTB;
		int numDeathsTBPulmHIVNegative;
		int numDeathsTBPulmHIVPositive[SimContext::CD4_NUM_STRATA];
		int numDeathsTBExtraPulmHIVNegative;
		int numDeathsTBExtraPulmHIVPositive[SimContext::CD4_NUM_STRATA];
		int numDeathsTBLTFUHIVNegative;
		int numDeathsTBLTFUHIVPositive[SimContext::CD4_NUM_STRATA];
		int numDeathsTBWhileFailedTBTreatment;
		int numAllDeathsWhileFailedTBTreatment;

		/** number alive at this time with CHRMs**/
		int numAliveWithCHRMs;
		/** number alive at this time without CHRMs**/
		int numAliveWithoutCHRMs;
		/** number alive at this time stratified by CHRM**/
		int numAliveCHRM[SimContext::CHRM_NUM];
		/** number alive at this time, stratified by Care state*/
		int numAliveCare[SimContext::HIV_CARE_NUM];
		/** number alive at this time, stratified by care state and CD4 age category*/
		int numAliveCareCD4Metric[SimContext::HIV_CARE_NUM][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** number alive at this time who are in care but off of art */
		int numAliveInCareOffART;
		/** number alive at this time who are in care but off of art stratified by CD4 metric*/
		int numAliveInCareOffARTCD4Metric[SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** number alive at this time who are positive */
		int numAlivePositive;
		/** number alive at this time who are positive by CD4 metric */
		int numAlivePositiveCD4Metric[SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** total number alive at this time who are on ART */
		int totalAliveOnART;
		/** number alive at this time who are on art startified by art line and supp */
		int numAliveOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		/** number alive at this time who are on art stratified by art line, supp, and CD4 metric */
		int numAliveOnARTCD4Metric[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES][SimContext::PEDS_CD4_AGE_CAT_NUM];
		/** number alive at this time with CHRMs, stratified by HIV state */
		int numAliveWithCHRMsDetState[SimContext::HIV_ID_NUM];
		/** number alive at this time withoutCHRMs, stratified by HIV state */
		int numAliveWithoutCHRMsDetState[SimContext::HIV_ID_NUM];
		/** number alive at this time, stratified by HIV state and CHRM*/
		int numAliveTypeCHRMs[SimContext::HIV_ID_NUM][SimContext::CHRM_NUM];
		/** number of pediatrics patients alive at this time, stratified by HIV state */
		int numAlivePediatrics[SimContext::PEDS_HIV_NUM];
		/** number of pediatrics patients with living mother stratified by maternal type */
		int numAlivePediatricsMotherAlive[SimContext::PEDS_MATERNAL_STATUS_NUM];
		/** number of pediatrics patients with dead mother */
		int numAlivePediatricsMotherDead;
		/** number of HIV negative pediatrics patients breastfeeding from an HIV+ mother this month */
		int numHIVExposedUninf[SimContext::PEDS_EXPOSED_BREASTFEEDING_NUM];
		/** number of pediatrics patients who have never been exposed to HIV this month */
		int numNeverHIVExposed;
		/** number of pediatrics patients that were detected this month with an alive mother with unknown status*/
		int numNewlyDetectedPediatricsMotherStatusUnknown;
		/** number of EID test results stratified by type of test*/
		int numEIDTestsGivenType[SimContext::EID_TEST_TYPE_NUM];
		int numTruePositiveEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];
		int numTrueNegativeEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];
		int numFalsePositiveEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];
		int numFalseNegativeEIDTestResultsType[SimContext::EID_TEST_TYPE_NUM];

		/** number of EID test results stratified by test num*/
		int numEIDTestsGivenTest[SimContext::EID_NUM_TESTS];
		int numTruePositiveEIDTestResultsTest[SimContext::EID_NUM_TESTS];
		int numTrueNegativeEIDTestResultsTest[SimContext::EID_NUM_TESTS];
		int numFalsePositiveEIDTestResultsTest[SimContext::EID_NUM_TESTS];
		int numFalseNegativeEIDTestResultsTest[SimContext::EID_NUM_TESTS];

		/** number of people who are false positives */
		int numAliveFalsePositive;
		int numAliveFalsePositiveLinked;

		/** Number of incident PP infections for peds */
		int numIncidentPPInfections;
		/** Number of incident HIV infections */
		int numIncidentHIVInfections;
		/** Number of incident HIV infections used for calculating dynamic transmissions, saved at the end of the warmup run and then used in the main run */
		int dynamicNumIncidentHIVInfections;
		/** Number of patient months spent at risk of HIV infection in primary cohort for debugging dynamic transmissions*/
		int debugNumHIVNegAtStartMonth;
		/** Number of patient months spent at risk of HIV infection used for calculating dynamic transmissions, saved at the end of the warmup run and then used in the main run */
		int dynamicNumHIVNegAtStartMonth;
		/** Self Transmission Rate Multiplier calculated in dynamic transmission (for output)*/
        double dynamicSelfTransmissionMult;
		/** Number of HIV-negative patients alive by HIV risk category*/
        int numAliveNegRisk[SimContext::HIV_BEHAV_NUM];
        /** Monthly probability of taking up PrEP for uninfected patients*/
        double probPrepUptake[SimContext::HIV_BEHAV_NUM];
		
		
		/** Number of HIV detections this month stratified by method of detection */
		int numHIVDetections[SimContext::HIV_DET_NUM];
		/** Cumulative number of HIV detections stratified by method of detection */
		int cumulativeNumHIVDetections[SimContext::HIV_DET_NUM];
		/** Number tested with user-defined HIV tests this time period */
		int numHIVTestsPerformed;
		/** Number tested with user-defined HIV tests at their initial test offer (Month 0 or when they reach the start age) */
		int numHIVTestsPerformedAtInitOffer;
		/** Number of user-defined HIV tests performed this time period excluding initial offers at screening startup */
		int numHIVTestsPerformedPostStartup;
		/** Total cumulative number of user-defined HIV tests conducted since simulation start */
		int cumulativeNumHIVTests;
		/** Cumulative number tested with user-defined HIV tests at their initial test offer (Month 0 or when they reach the starting age)  */
		int cumulativeNumHIVTestsAtInitOffer;
		/** Cumulative number of user-defined HIV tests conducted post-startup month (excluded initial offers) */
		int cumulativeNumHIVTestsPostStartup;
		
		/** Number of incident Chrms stratified by chrm*/
		int numIncidentCHRMs[SimContext::CHRM_NUM];
		/** Number with OI history stratified by type*/
		int numWithOIHistExt[SimContext::HIST_EXT_NUM];
		int numWithOIHistExtCare[SimContext::HIST_EXT_NUM][SimContext::HIV_CARE_NUM];
		int numWithOIHistExtInCareOffART[SimContext::HIST_EXT_NUM];
		int numWithOIHistExtOnART[SimContext::HIST_EXT_NUM][SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		int numWithOIHistExtPositive[SimContext::HIST_EXT_NUM];
		/** Number of each gender*/
		int numGender[SimContext::GENDER_NUM];
		int numGenderCare[SimContext::GENDER_NUM][SimContext::HIV_CARE_NUM];
		int numGenderInCareOffART[SimContext::GENDER_NUM];
		int numGenderOnART[SimContext::GENDER_NUM][SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		int numGenderPositive[SimContext::GENDER_NUM];
		/** Sum of all QOL modifiers applied that month -- reported at Ben Linas's request, 2/3/2010 -- errhode */
		double sumQOLModifiers;

		/** Prop respond stratified by care state */
		/** HIV-negative patients draw a baseline PTR logit value, but their PTR isn't used until they become HIV+ */
		double propRespSum;
		double propRespMean;
		double propRespSumSquares;
		double propRespStdDev;
		double propRespSumCare[SimContext::HIV_CARE_NUM];
		double propRespMeanCare[SimContext::HIV_CARE_NUM];
		double propRespSumSquaresCare[SimContext::HIV_CARE_NUM];
		double propRespStdDevCare[SimContext::HIV_CARE_NUM];
		double propRespSumInCareOffART;
		double propRespSumOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double propRespSumPositive;
		double propRespMeanInCareOffART;
		double propRespMeanOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double propRespMeanPositive;
		double propRespSumSquaresInCareOffART;
		double propRespSumSquaresOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double propRespSumSquaresPositive;
		double propRespStdDevInCareOffART;
		double propRespStdDevOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double propRespStdDevPositive;

		/** age stratified by care state */
		double ageSum;
		double ageMean;
		double ageSumSquares;
		double ageStdDev;
		double ageSumCare[SimContext::HIV_CARE_NUM];
		double ageMeanCare[SimContext::HIV_CARE_NUM];
		double ageSumSquaresCare[SimContext::HIV_CARE_NUM];
		double ageStdDevCare[SimContext::HIV_CARE_NUM];
		double ageSumInCareOffART;
		double ageSumOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double ageSumPositive;
		double ageMeanInCareOffART;
		double ageMeanOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double ageMeanPositive;
		double ageSumSquaresInCareOffART;
		double ageSumSquaresOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double ageSumSquaresPositive;
		double ageStdDevInCareOffART;
		double ageStdDevOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double ageStdDevPositive;

		// Monthly Age-Stratified HIV/Care Status Outputs
        int numAgeBracketCare[SimContext::HIV_CARE_NUM][SimContext::OUTPUT_AGE_CAT_NUM];
		int numAgeBracketOnART[SimContext::OUTPUT_AGE_CAT_NUM];
		int numAgeBracketInCareOffART[SimContext::OUTPUT_AGE_CAT_NUM];
		int numAgeBracketHIVPositive[SimContext::OUTPUT_AGE_CAT_NUM];
		int numAgeBracketAlive[SimContext::OUTPUT_AGE_CAT_NUM];
		int numDeathsAgeBracketCare[SimContext::HIV_CARE_NUM][SimContext::OUTPUT_AGE_CAT_NUM];
		int numDeathsAgeBracketOnART[SimContext::OUTPUT_AGE_CAT_NUM];
		int numDeathsAgeBracketInCareOffART[SimContext::OUTPUT_AGE_CAT_NUM];
		int numDeathsAgeBracketHIVPositive[SimContext::OUTPUT_AGE_CAT_NUM];
		int numDeathsAgeBracket[SimContext::OUTPUT_AGE_CAT_NUM];

		// true and observed CD4 and HVL
		/** Total true CD4 for HIV+ patients Average true CD4 for HIV+ patients (Absolute CD4 metric only) this month */
		double trueCD4Sum;
		/** Average true CD4 for HIV+ patients (Absolute CD4 metric only) this month */
		double trueCD4Mean;
		/** Total sum of squares of true CD4 for HIV+ patients this month */
		double trueCD4SumSquares;
		/** Standard deviation of true CD4 for HIV+ patients this month */
		double trueCD4StdDev;
		/** True CD4 (Absolute CD4 metric only) stratified by care status - includes HIV- for inclusion in output tables with other inputs that do apply to HIV- patients but only HIV+ patients should be included in calculations since HIV- patients have no CD4 counts */
		double trueCD4SumCare[SimContext::HIV_CARE_NUM];
		double trueCD4MeanCare[SimContext::HIV_CARE_NUM];
		double trueCD4SumSquaresCare[SimContext::HIV_CARE_NUM];
		double trueCD4StdDevCare[SimContext::HIV_CARE_NUM];
		double trueCD4SumInCareOffART;
		double trueCD4SumOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double trueCD4MeanInCareOffART;
		double trueCD4MeanOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double trueCD4SumSquaresInCareOffART;
		double trueCD4SumSquaresOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double trueCD4StdDevInCareOffART;
		double trueCD4StdDevOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];

		/** Total observed CD4 in HIV+ patients with absolute CD4 counts this month */
		double observedCD4Sum;
		/** Average observed CD4 in HIV+ patients with absolute CD4 counts this month */
		double observedCD4Mean;
		/** Total sum of squares of observed CD4 in HIV+ patients with absolute CD4 counts this month */
		double observedCD4SumSquares;
		/** Standard deviation of observed CD4 in HIV+ patients with absolute CD4 counts this month */
		double observedCD4StdDev;
		/** observed CD4 stratified by care status - HIV- patients are included because the outputs go into tables that contain other inputs applicable to HIV- patients but only HIV+ patients have observed CD4 counts so HIV- patients should not be included in calculations */
		double observedCD4SumCare[SimContext::HIV_CARE_NUM];
		double observedCD4MeanCare[SimContext::HIV_CARE_NUM];
		double observedCD4SumSquaresCare[SimContext::HIV_CARE_NUM];
		double observedCD4StdDevCare[SimContext::HIV_CARE_NUM];
		double observedCD4SumInCareOffART;
		double observedCD4SumOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double observedCD4MeanInCareOffART;
		double observedCD4MeanOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double observedCD4SumSquaresInCareOffART;
		double observedCD4SumSquaresOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		double observedCD4StdDevInCareOffART;
		double observedCD4StdDevOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		/** Total true CD4 percentage (Peds early patients) this month */
		double trueCD4PercentageSum;
		/** Average true CD4 percentage (Peds early patients) this month */
		double trueCD4PercentageMean;
		/** Total sum of squares of true CD4 percentage (Peds early patients) this month */
		double trueCD4PercentageSumSquares;
		/** Standard deviation of true CD4 percentage (Peds early patients) this month */
		double trueCD4PercentageStdDev;
		/** Total true HVL this month */
		double trueHVLSum;
		/** Average true HVL this month */
		double trueHVLMean;
		/** Total sum of squares of true HVL this month */
		double trueHVLSumSquares;
		/** Standard deviation of true HVL this month */
		double trueHVLStdDev;
		/** Total observed HVL this month */
		double observedHVLSum;
		/** Average observed HVL this month */
		double observedHVLMean;
		/** Total sum of squares of observed HVL this month */
		double observedHVLSumSquares;
		/** Standard deviation of observed HVL this month */
		double observedHVLStdDev;
		/** distribution of true CD4 stratified by ART state x CD4 */
		int trueCD4ARTDistribution[SimContext::ART_NUM_STATES][SimContext::CD4_NUM_STRATA];
		/** distribution of observed CD4 stratified by CD4 */
		int observedCD4Distribution[SimContext::CD4_NUM_STRATA];
		/** distribution of observed CD4 stratifie by CD4 and Care state */
		int observedCD4DistributionCare[SimContext::CD4_NUM_STRATA][SimContext::HIV_CARE_NUM];
		/** distribution of observed CD4 stratified by art line and efficacy */
		int observedCD4DistributionOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		/** number of HIV+ patients with observed CD4 who are off art in care */
		int numWithObservedCD4InCareOffART;
		/** number of HIV+ patients with observed CD4 */
		int numHIVPosWithObservedCD4;

		/** distribution of true HVL stratified by HVL */
		int trueHVLDistribution[SimContext::HVL_NUM_STRATA];
		/** distribution of observed HVL stratified by HVL */
		int observedHVLDistribution[SimContext::HVL_NUM_STRATA];
		/** distribution of true CD4/HVL stratified by ART state x CD4 x HVL */
		int trueCD4HVLARTDistribution[SimContext::ART_NUM_STATES][SimContext::CD4_NUM_STRATA][SimContext::HVL_NUM_STRATA];
		/** number of transmissions per month calculated by community viral load */
		double numTransmissions;
		double numTransmissionsHVL[SimContext::HVL_NUM_STRATA];
		double numTransmissionsRisk[SimContext::TRANSM_RISK_NUM];
		/** number in each ART efficacy state */
		int numARTEfficacyState[SimContext::ART_EFF_NUM_TYPES];
		/** number with primary OIs, stratified by OI type */
		int numPrimaryOIs[SimContext::OI_NUM];
		/** number with secondary OIs, stratified by OI type */
		int numSecondaryOIs[SimContext::OI_NUM];
		/** total across all OI types of primary OI incidence */
		int numPrimaryOIsTotal;
		/** total across all OI types of secondary OI incidence */
		int numSecondaryOIsTotal;
		/** total primary + secondary events across all OI types */
		int numOIsTotal;
		/** number with OI history by type */
		int numWithOIHistory[SimContext::OI_NUM];
		/** number without any OI history - includes HIVneg  */
		int numWithoutOIHistory;
		/** number with first OI , stratified by OI type */
		int numWithFirstOI[SimContext::OI_NUM];
		/** total number of deaths*/
		int numDeaths;
		/** deaths by care state*/
		int numDeathsCare[SimContext::HIV_CARE_NUM];
		/** deaths who are in care but off of art */
		int numDeathsInCareOffART;
		/** total deaths who are on art */
		int totalDeathsOnART;
		/** deaths who are on art stratified by art line and supp */
		int numDeathsOnART[SimContext::ART_NUM_LINES][SimContext::ART_EFF_NUM_TYPES];
		int numDeathsPositive;
		/** number of people with chrms stratified by Age */
		int numCHRMsAgeTotal[SimContext::CHRM_AGE_CAT_NUM];
		/** number of people with chrms stratified by Gender */
		int numCHRMsGenderTotal[SimContext::GENDER_NUM];
		/** number of people with chrms stratified by cd4 */
		int numCHRMsCD4Total[SimContext::CD4_NUM_STRATA];
		/** number with specific CHRM stratified by Age*/
		int numCHRMsAge[SimContext::CHRM_NUM][SimContext::CHRM_AGE_CAT_NUM];
		/** number with specific CHRM stratified by Sex*/
		int numCHRMsGender[SimContext::CHRM_NUM][SimContext::GENDER_NUM];
		/** number with specific CHRM stratified by CD4*/
		int numCHRMsCD4[SimContext::CHRM_NUM][SimContext::CD4_NUM_STRATA];
		/** deaths from first OI, stratified by OI type */
		int numDeathsFromFirstOI[SimContext::OI_NUM];
		/** num of deaths by cause of death type */
		int numDeathsType[SimContext::DTH_NUM_CAUSES];
		/** num of deaths of HIV + by cause of death type */
		int numHIVPosDeathsType[SimContext::DTH_NUM_CAUSES];
		/** num of deaths by cause of death type and care state */
		int numDeathsTypeCare[SimContext::DTH_NUM_CAUSES][SimContext::HIV_CARE_NUM];
		/** Number of deaths of patients with CHRMs stratified by death cause and CHRM type**/
		int numDeathsWithCHRMsTypeCHRM[SimContext::DTH_NUM_CAUSES][SimContext::CHRM_NUM];
		/**number of deaths of patients with chrms stratified by chrm type*/
		int numDeathsWithCHRMsCHRM[SimContext::CHRM_NUM];
		/** Number of deaths of patients without CHRMs stratified by death cause**/
		int numDeathsWithoutCHRMsType[SimContext::DTH_NUM_CAUSES];
		/**Total number of deaths of patients without chrms*/
		int numDeathsWithoutCHRMs;
		// costs of various testing and total monthly cost
		/** Monthly costs of CD4 testing */
		double costsCD4Testing;
		/** Monthly costs of HVL testing */
		double costsHVLTesting;
		/** Monthly costs of clinic visits */
		double costsClinicVisits;
		/** Monthly costs for EID visits */
		double costsEIDVisits;
		/** Monthly PrEP costs */
		double costsPrEP;
		/** Monthly costs of HIV testing */
		double costsHIVTests;
		/** Monthly costs of miscellaneous HIV */
		double costsHIVMisc;
		/** Monthly costs of Lab Staging Testing */
		double costsLabStagingTests;
		/** Monthly Costs for EID tests */
		double costsEIDTests;
		/** Monthly costs for Infant HIV Proph Administration */
		double costsInfantHIVProphDirect;
		/** Monthly costs for Infant HIV Proph Toxicity*/
		double costsInfantHIVProphTox;
		/** Monthly costs of miscellaneous Lab Staging */
		double costsLabStagingMisc;
		/** Monthly Costs for EID misc costs */
		double costsEIDMisc;
		/**costs due to adherence interventions*/
		double costsInterventionStartup;
		double costsInterventionMonthly;

		/** Monthly costs total */
		double totalMonthlyCohortCosts;
		/** Monthly TB costs total */
		double totalMonthlyTBCohortCosts;
		/** Total discounted costs stratified by cost type */
		double totalMonthlyCohortCostsType[SimContext::COST_NUM_TYPES];
		/** costs of prophylaxis, stratified by OI type x proph line */
		double costsProph[SimContext::OI_NUM][SimContext::PROPH_NUM];
		/** costs of ART, stratified by ART line */
		double costsART[SimContext::ART_NUM_LINES];
		/** costs of CHRMs, stratified by CHRM */
		double costsCHRMs[SimContext::CHRM_NUM];
		/** cumulative costs up to month */
		double cumulativeCohortCosts;
		double cumulativeCohortCostsType[SimContext::COST_NUM_TYPES];
		double cumulativeARTCosts;
		double cumulativeCD4TestingCosts;
		double cumulativeHVLTestingCosts;
		double cumulativeHIVTestingCosts;
		double cumulativeHIVMiscCosts;

		/** Number on PrEP */
		int numOnPrEP[SimContext::HIV_BEHAV_NUM];
		/** Number of Incident Toxicities by ART, Subregimen, Tox Type, Tox-Num**/
		int incidentToxicities[SimContext::ART_NUM_LINES][SimContext::ART_NUM_SUBREGIMENS][SimContext::ART_NUM_TOX_SEVERITY][SimContext::ART_NUM_TOX_PER_SEVERITY];
		/** Number of Prevalent Chronic Toxicities by ART, Subregimen, Tox-Num**/
		int prevalentChronicToxicities[SimContext::ART_NUM_LINES][SimContext::ART_NUM_SUBREGIMENS][SimContext::ART_NUM_TOX_PER_SEVERITY];
		/** Number on ART, stratified by ART line */
		int numOnART[SimContext::ART_NUM_LINES];
		/** Number of HIV+ in_care who are pre-ART */
		int numInCarePreART;
		/** Number of HIV+ in care who are post-ART */
		int numInCarePostART;
		/** Number starting particular ART line this month, stratified by ART line */
		int numStartingART[SimContext::ART_NUM_LINES];
		/** Number of HIV+ in_care who are starting pre-ART this month */
		int numStartingPreART;
		/** Number of HIV+ in care who are starting post-ART this month*/
		int numStartingPostART;
		/** Number lost to follow up stratified by ART line */
		int numLostToFollowUpART[SimContext::ART_NUM_LINES];
		/** Total number of people becoming lost this month */
		int numStartingLostToFollowUpART[SimContext::ART_NUM_LINES];
		/** Number lost to follow up who are pre-ART */
		int numLostToFollowUpPreART;
		/** Total number of people becoming lost this month who are pre art*/
		int numStartingLostToFollowUpPreART;
		/** Number lost to follow up who are post-ART */
		int numLostToFollowUpPostART;
		/** Total number of people becoming lost this month who are post-ART*/
		int numStartingLostToFollowUpPostART;
		/** number return to care on prev ART line, stratified by ART line */
		int numReturnOnPrevART[SimContext::ART_NUM_LINES];
		/** number return to care on subsequent ART line, stratified by ART line */
		int numReturnOnNextART[SimContext::ART_NUM_LINES];
		/** number return to care who are pre-ART */
		int numReturnToCarePreART;
		/** number return to care who are post-ART */
		int numReturnToCarePostART;
		/** num of death while LTFU stratified by ART line */
		int numDeathsWhileLostART[SimContext::ART_NUM_LINES];
		/** num of death while LTFU who are pre-ART */
		int numDeathsWhileLostPreART;
		/** num of death while LTFU who are post-ART */
		int numDeathsWhileLostPostART;
		/** num of deaths HIV+ who never visited clinic (includes those linked to care who die before first visit) */
		int numDeathsHIVPosNeverVisitedClinic;
		/** num of deaths HIV+ who had at least one clinic visit since model start*/
		int numDeathsHIVPosHadClinicVisit;
		/** num of death hiv negative */
		int numDeathsUninfected;
	}; /* end TimeSummary */

	/** OrphanStats class contains orphan stats */
	class OrphanStats {
	public:
		/** Time period month*/
		int timePeriod;
		/** number of orphans upon death of patient*/
		int numOrphans;
		/** number of orphans upon death of patient stratified by orphan age */
		int numOrphansAge[SimContext::CHRM_ORPHANS_OUTPUT_AGE_CAT_NUM];
	}; /* end OrphanStats */

	/* Accessor functions returning const pointers to the statistics subclass objects */
	const PopulationSummary *getPopulationSummary();
	const HIVScreening *getHIVScreening();
	const SurvivalStats *getSurvivalStats(int groupType);
	const InitialDistributions *getInitialDistributions();
	const CHRMsStats *getCHRMsStats();
	const OIStats *getOIStats();
	const DeathStats *getDeathStats();
	const OverallSurvival *getOverallSurvival();
	const OverallCosts *getOverallCosts();
	const TBStats *getTBStats();
	const LTFUStats *getLTFUStats();
	const ProphStats *getProphStats();
	const ARTStats *getARTStats();
	const TimeSummary *getTimeSummary(unsigned int timePeriod);
	const OrphanStats * getOrphanStats(unsigned int timePeriod);

	/* Functions to calculate final aggregate statistics and to write out the stats file */
	void initRunStats(bool isDynamic);
	void finalizeStats();
	void writeStatsFile();

private:
	/** Pointer to the associated simulation context */
	SimContext *simContext;
	/** Stats file name */
	string statsFileName;
	/** Stats file pointer */
	FILE *statsFile;

	/** Orphans output file name */
	string orphanFileName;
	/** Orphans output file pointer */
	FILE *orphanFile;

	/** Statistics subclass object */
	PopulationSummary popSummary;
	/** Statistics subclass object */
	HIVScreening hivScreening;
	/** Statistics subclass object */
	SurvivalStats survivalStats[NUM_SURVIVAL_GROUPS];
	/** Statistics subclass object */
	InitialDistributions initialDistributions;
	/** Statistics subclass object */
	CHRMsStats chrmsStats;
	/** Statistics subclass object */
	OIStats oiStats;
	/** Statistics subclass object */
	DeathStats deathStats;
	/** Statistics subclass object */
	OverallSurvival overallSurvival;
	/** Statistics subclass object */
	OverallCosts overallCosts;
	/** Statistics subclass object */
	TBStats tbStats;
	/** Statistics subclass object */
	LTFUStats ltfuStats;
	/** Statistics subclass object */
	ProphStats prophStats;
	/** Statistics subclass object */
	ARTStats artStats;
	/** vector of PatientSummary objects for all cohorts in this context,
	//	uses actual object sinces subclass only contains 3 native type members, copy is cheap */
	vector<PatientSummary> patients;
	/** vector of TimeSummary object for each month/year time period,
	//	use pointer to object since subclass is complex and copy would be expensive */
	vector<TimeSummary *> timeSummaries;
	/** Orphan statistics subclass object */
	vector<OrphanStats *> orphanStats;

	/* Initialization functions for statistics objects, called by constructor */
	void initPopulationSummary();
	void initHIVScreening();
	void initSurvivalStats();
	void initInitialDistributions();
	void initCHRMsStats();
	void initOIStats();
	void initDeathStats();
	void initOverallSurvival();
	void initOverallCosts();
	void initTBStats();
	void initLTFUStats();
	void initProphStats();
	void initARTStats();
	void initTimeSummary(TimeSummary *currTime, bool isDynamic = false);
	void initOrphanStats(OrphanStats *currTime);

	/* Functions to finalize aggregate statistics before printing out */
	void finalizePopulationSummary();
	void finalizeHIVScreening();
	void finalizeSurvivalStats();
	void finalizeInitialDistributions();
	void finalizeCHRMsStats();
	void finalizeOIStats();
	void finalizeDeathStats();
	void finalizeOverallSurvival();
	void finalizeOverallCosts();
	void finalizeTBStats();
	void finalizeLTFUStats();
	void finalizeProphStats();
	void finalizeARTStats();
	void finalizeTimeSummaries();

	/* Functions to write out each subclass object to the statistics file, called by writeStatsFile */
	void writePopulationSummary();
	void writeHIVScreening();
	void writeSurvivalStats();
	void writeInitialDistributions();
	void writeCHRMsStats();
	void writeOIStats();
	void writeDeathStats();
	void writeOverallSurvival();
	void writeOverallCosts();
	void writeTBStats();
	void writeLTFUStats();
	void writeProphStats();
	void writeARTStats();
	void writeTimeSummaries();
	void writeOrphanStats();
};

/** \brief getPopulationSumary returns a const pointer to the PopulationSummary statistics object */
inline const RunStats::PopulationSummary *RunStats::getPopulationSummary() {
	return &popSummary;
}

/** \brief getHIVScreening returns a const pointer to the HIVScreening statistics object */
inline const RunStats::HIVScreening *RunStats::getHIVScreening() {
	return &hivScreening;
}


/** \brief getSurvivalStats returns a const pointer to the specified subgroup's SurvivalStats object */
inline const RunStats::SurvivalStats *RunStats::getSurvivalStats(int groupType) {
	return &(survivalStats[groupType]);
}

/** \brief getInitialDistributions returns a const pointer to the InitialDistributions object */
inline const RunStats::InitialDistributions *RunStats::getInitialDistributions() {
	return &initialDistributions;
}

/** \brief getOIStats returns a const pointer to the CHRMsStats object */
inline const RunStats::CHRMsStats *RunStats::getCHRMsStats() {
	return &chrmsStats;
}

/** \brief getOIStats returns a const pointer to the OIStats object */
inline const RunStats::OIStats *RunStats::getOIStats() {
	return &oiStats;
}

/** \brief getDeathStats returns a const pointer to the DeathStats object */
inline const RunStats::DeathStats *RunStats::getDeathStats() {
	return &deathStats;
}

/** \brief getOverallSurvival returns a const pointer to the OverallSurvival object */
inline const RunStats::OverallSurvival *RunStats::getOverallSurvival() {
	return &overallSurvival;
}

/** \brief getOverallCosts returns a const pointer to the OverallCosts object */
inline const RunStats::OverallCosts *RunStats::getOverallCosts() {
	return &overallCosts;
}

/** \brief getTBStats returns a const pointer to the TBStats object */
inline const RunStats::TBStats *RunStats::getTBStats() {
	return &tbStats;
}

/** \brief getLTFUStats returns a const pointer to the LTFUStats object */
inline const RunStats::LTFUStats *RunStats::getLTFUStats() {
	return &ltfuStats;
}

/** \brief getProphStats returns a const pointer to the ProphStats object */
inline const RunStats::ProphStats *RunStats::getProphStats() {
	return &prophStats;
}

/** \brief getARTStats returns a const pointer to the ArtStats object */
inline const RunStats::ARTStats *RunStats::getARTStats() {
	return &artStats;
}

/** \brief getTimeSummary returns a const pointer to the specified TimeSummary object,
	returns null if one does not exist for this time period */
inline const RunStats::TimeSummary *RunStats::getTimeSummary(unsigned int timePeriod) {
	if (timePeriod < timeSummaries.size())
		return timeSummaries[timePeriod];
	return NULL;
}

/** \brief getOrphanStats returns a const pointer to the OrphanStats object */
inline const RunStats::OrphanStats *RunStats::getOrphanStats(unsigned int timePeriod) {
	if (timePeriod < orphanStats.size())
		return orphanStats[timePeriod];
	return NULL;
}