CovidSim.cpp

/*
(c) 2004-20 Neil Ferguson, Imperial College London (neil.ferguson@imperial.ac.uk)
*/
 
#include <errno.h>
#include <stddef.h>
 
#include "CovidSim.h"
#include "BinIO.h"
#include "Rand.h"
#include "Error.h"
#include "Dist.h"
#include "Kernels.h"
#include "Bitmap.h"
#include "Model.h"
#include "Param.h"
#include "SetupModel.h"
#include "ModelMacros.h"
#include "InfStat.h"
#include "CalcInfSusc.h"
#include "Update.h"
#include "Sweep.h"
 
#ifdef _OPENMP
#include <omp.h>
#endif // _OPENMP
 
// Use the POSIX name for case-insensitive string comparison: strcasecmp.
#ifdef _WIN32
// Windows calls it _stricmp so make strcasecmp an alias.
#include <string.h>
#define strcasecmp _stricmp
#else
#include <strings.h>
#endif
 
void ReadParams(char*, char*);
void ReadInterventions(char*);
int GetXMLNode(FILE*, const char*, const char*, char*, int);
void ReadAirTravel(char*);
void InitModel(int); //adding run number as a parameter for event log: ggilani - 15/10/2014
void SeedInfection(double, int*, int, int); //adding run number as a parameter for event log: ggilani - 15/10/2014
int RunModel(int); //adding run number as a parameter for event log: ggilani - 15/10/2014
 
void SaveDistribs(void);
void SaveOriginDestMatrix(void); //added function to save origin destination matrix so it can be done separately to the main results: ggilani - 13/02/15
void SaveResults(void);
void SaveSummaryResults(void);
void SaveRandomSeeds(void); //added this function to save random seeds for each run: ggilani - 09/03/17
void SaveEvents(void); //added this function to save infection events from all realisations: ggilani - 15/10/14
void LoadSnapshot(void);
void SaveSnapshot(void);
void RecordInfTypes(void);
void RecordSample(double, int);
 
void CalcOriginDestMatrix_adunit(void); //added function to calculate origin destination matrix: ggilani 28/01/15
 
int GetInputParameter(FILE*, FILE*, const char*, const char*, void*, int, int, int);
int GetInputParameter2(FILE*, FILE*, const char*, const char*, void*, int, int, int);
int GetInputParameter3(FILE*, const char*, const char*, void*, int, int, int);
 
void SetICDF(double* icdf, double startValue);
 

 
Param P;
Person* Hosts;
Household* Households;
PopVar State, StateT[MAX_NUM_THREADS];
Cell* Cells; // Cells[i] is the i'th cell
Cell ** CellLookup; // CellLookup[i] is a pointer to the i'th populated cell
Microcell* Mcells, ** McellLookup;
Place** Places;
AdminUnit AdUnits[MAX_ADUNITS];
Results* TimeSeries, * TSMean, * TSVar, * TSMeanNE, * TSVarNE, * TSMeanE, * TSVarE; 
Airport* Airports;
BitmapHeader* bmh;
//added declaration of pointer to events log: ggilani - 10/10/2014
Events* InfEventLog;
int nEvents;
 
double inftype[INFECT_TYPE_MASK], inftype_av[INFECT_TYPE_MASK], infcountry[MAX_COUNTRIES], infcountry_av[MAX_COUNTRIES], infcountry_num[MAX_COUNTRIES];
double indivR0[MAX_SEC_REC][MAX_GEN_REC], indivR0_av[MAX_SEC_REC][MAX_GEN_REC];
double inf_household[MAX_HOUSEHOLD_SIZE + 1][MAX_HOUSEHOLD_SIZE + 1], denom_household[MAX_HOUSEHOLD_SIZE + 1];
double inf_household_av[MAX_HOUSEHOLD_SIZE + 1][MAX_HOUSEHOLD_SIZE + 1], AgeDist[NUM_AGE_GROUPS], AgeDist2[NUM_AGE_GROUPS];
double case_household[MAX_HOUSEHOLD_SIZE + 1][MAX_HOUSEHOLD_SIZE + 1], case_household_av[MAX_HOUSEHOLD_SIZE + 1][MAX_HOUSEHOLD_SIZE + 1];
double PropPlaces[NUM_AGE_GROUPS * AGE_GROUP_WIDTH][NUM_PLACE_TYPES];
double PropPlacesC[NUM_AGE_GROUPS * AGE_GROUP_WIDTH][NUM_PLACE_TYPES], AirTravelDist[MAX_DIST];
double PeakHeightSum, PeakHeightSS, PeakTimeSum, PeakTimeSS;
 
// These allow up to about 2 billion people per pixel, which should be ample.
int32_t *bmPopulation; // The population in each bitmap pixel. Special value -1 means "country boundary"
int32_t *bmInfected; // The number of infected people in each bitmap pixel.
int32_t *bmRecovered; // The number of recovered people in each bitmap pixel.
int32_t *bmTreated; // The number of treated people in each bitmap pixel.
 
char OutFile[1024], OutFileBase[1024], OutDensFile[1024], SnapshotLoadFile[1024], SnapshotSaveFile[1024], AdunitFile[1024];
 
int ns, DoInitUpdateProbs, InterruptRun = 0;
int PlaceDistDistrib[NUM_PLACE_TYPES][MAX_DIST], PlaceSizeDistrib[NUM_PLACE_TYPES][MAX_PLACE_SIZE];
 
 
/* int NumPC,NumPCD; */
const int MAXINTFILE = 10;
 
/* default start value for icdf arrays */
const int ICDF_START = 100;
 
int main(int argc, char* argv[])
{
    char ParamFile[1024]{}, DensityFile[1024]{}, NetworkFile[1024]{}, AirTravelFile[1024]{}, SchoolFile[1024]{}, RegDemogFile[1024]{}, InterventionFile[MAXINTFILE][1024]{}, PreParamFile[1024]{}, buf[2048]{}, * sep;
    int i, GotP, GotPP, GotO, GotL, GotS, GotAP, GotScF, GotNR, Perr, cl;

    GotP = GotO = GotL = GotS = GotAP = GotScF = GotPP = GotNR = 0;
 
    Perr = 0;
    fprintf(stderr, "sizeof(int)=%i sizeof(long)=%i sizeof(float)=%i sizeof(double)=%i sizeof(unsigned short int)=%i sizeof(int *)=%i\n", (int)sizeof(int), (int)sizeof(long), (int)sizeof(float), (int)sizeof(double), (int)sizeof(unsigned short int), (int)sizeof(int*));
    cl = clock();
 
    // Default bitmap format is platform dependent.
#if defined(IMAGE_MAGICK) || defined(_WIN32)
    P.BitmapFormat = BF_PNG;
#else
    P.BitmapFormat = BF_BMP;
#endif

 
    if (argc < 7)   Perr = 1;
    else
    {
        i = argc - 4;
        sscanf(argv[i], "%i", &P.setupSeed1);
        sscanf(argv[i + 1], "%i", &P.setupSeed2);
        sscanf(argv[i + 2], "%i", &P.runSeed1);
        sscanf(argv[i + 3], "%i", &P.runSeed2);

        P.PlaceCloseIndepThresh = P.LoadSaveNetwork = P.DoHeteroDensity = P.DoPeriodicBoundaries = P.DoSchoolFile = P.DoAdunitDemog = P.OutputDensFile = P.MaxNumThreads = P.DoInterventionFile = 0;
        P.PreControlClusterIdCaseThreshold = 0;
        P.R0scale = 1.0;
        P.KernelOffsetScale = P.KernelPowerScale = 1.0; //added this so that kernel parameters are only changed if input from the command line: ggilani - 15/10/2014
        P.DoSaveSnapshot = P.DoLoadSnapshot  = 0;

        for (i = 1; i < argc - 4; i++)
        {
            if ((argv[i][0] != '/') && ((argv[i][2] != ':') && (argv[i][3] != ':'))) Perr = 1;
            if (argv[i][1] == 'P' && argv[i][2] == ':')
            {
                GotP = 1;
                sscanf(&argv[i][3], "%s", ParamFile);
            }
            else if (argv[i][1] == 'O' && argv[i][2] == ':')
            {
                GotO = 1;
                sscanf(&argv[i][3], "%s", OutFileBase);
            }
            else if (argv[i][1] == 'D' && argv[i][2] == ':')
            {
                sscanf(&argv[i][3], "%s", DensityFile);
                P.DoHeteroDensity = 1;
                P.DoPeriodicBoundaries = 0;
            }
            else if (argv[i][1] == 'A' && argv[i][2] == ':')
            {
                sscanf(&argv[i][3], "%s", AdunitFile);
            }
            else if (argv[i][1] == 'L' && argv[i][2] == ':')
            {
                GotL = 1;
                P.LoadSaveNetwork = 1;
                sscanf(&argv[i][3], "%s", NetworkFile);
            }
            else if (argv[i][1] == 'S' && argv[i][2] == ':')
            {
                P.LoadSaveNetwork = 2;
                GotS = 1;
                sscanf(&argv[i][3], "%s", NetworkFile);
            }
            else if (argv[i][1] == 'R' && argv[i][2] == ':')
            {
                sscanf(&argv[i][3], "%lf", &P.R0scale);
            }
            else if (argv[i][1] == 'N' && argv[i][2] == 'R' && argv[i][3] == ':')
            {
                sscanf(&argv[i][4], "%i", &GotNR);
            }
            else if (argv[i][1] == 'K' && argv[i][2] == 'P' && argv[i][3] == ':') //added Kernel Power and Offset scaling so that it can easily be altered from the command line in order to vary the kernel quickly: ggilani - 15/10/14
            {
                sscanf(&argv[i][4], "%lf", &P.KernelPowerScale);
            }
            else if (argv[i][1] == 'K' && argv[i][2] == 'O' && argv[i][3] == ':')
            {
                sscanf(&argv[i][4], "%lf", &P.KernelOffsetScale);
            }
            else if (argv[i][1] == 'C' && argv[i][2] == 'L' && argv[i][3] == 'P' && argv[i][4] == '1' && argv[i][5] == ':') // generic command line specified param - matched to #1 in param file
            {
                sscanf(&argv[i][6], "%lf", &P.clP1);
            }
            else if (argv[i][1] == 'C' && argv[i][2] == 'L' && argv[i][3] == 'P' && argv[i][4] == '2' && argv[i][5] == ':') // generic command line specified param - matched to #2 in param file
            {
                sscanf(&argv[i][6], "%lf", &P.clP2);
            }
            else if(argv[i][1] == 'C' && argv[i][2] == 'L' && argv[i][3] == 'P' && argv[i][4] == '3' && argv[i][5] == ':') // generic command line specified param - matched to #3 in param file
                {
                sscanf(&argv[i][6], "%lf", &P.clP3);
                }
            else if(argv[i][1] == 'C' && argv[i][2] == 'L' && argv[i][3] == 'P' && argv[i][4] == '4' && argv[i][5] == ':') // generic command line specified param - matched to #4 in param file
                {
                sscanf(&argv[i][6], "%lf", &P.clP4);
                }
            else if(argv[i][1] == 'C' && argv[i][2] == 'L' && argv[i][3] == 'P' && argv[i][4] == '5' && argv[i][5] == ':') // generic command line specified param - matched to #5 in param file
                {
                sscanf(&argv[i][6], "%lf", &P.clP5);
                }
            else if(argv[i][1] == 'C' && argv[i][2] == 'L' && argv[i][3] == 'P' && argv[i][4] == '6' && argv[i][5] == ':') // generic command line specified param - matched to #6 in param file
                {
                sscanf(&argv[i][6], "%lf", &P.clP6);
                }
            else if (argv[i][1] == 'A' && argv[i][2] == 'P' && argv[i][3] == ':')
            {
                GotAP = 1;
                sscanf(&argv[i][3], "%s", AirTravelFile);
            }
            else if (argv[i][1] == 's' && argv[i][2] == ':')
            {
                GotScF = 1;
                sscanf(&argv[i][3], "%s", SchoolFile);
            }
            else if (argv[i][1] == 'T' && argv[i][2] == ':')
            {
                sscanf(&argv[i][3], "%i", &P.PreControlClusterIdCaseThreshold);
            }
            else if (argv[i][1] == 'C' && argv[i][2] == ':')
            {
                sscanf(&argv[i][3], "%i", &P.PlaceCloseIndepThresh);
            }
            else if (argv[i][1] == 'd' && argv[i][2] == ':')
            {
                P.DoAdunitDemog = 1;
                sscanf(&argv[i][3], "%s", RegDemogFile);
            }
            else if (argv[i][1] == 'c' && argv[i][2] == ':')
            {
                sscanf(&argv[i][3], "%i", &P.MaxNumThreads);
            }
            else if (argv[i][1] == 'M' && argv[i][2] == ':')
            {
                P.OutputDensFile = 1;
                sscanf(&argv[i][3], "%s", OutDensFile);
            }
            else if (argv[i][1] == 'I' && argv[i][2] == ':')
            {
                sscanf(&argv[i][3], "%s", InterventionFile[P.DoInterventionFile]);
                P.DoInterventionFile++;
            }
            else if (argv[i][1] == 'L' && argv[i][2] == 'S' && argv[i][3] == ':')
            {
                sscanf(&argv[i][4], "%s", SnapshotLoadFile);
                P.DoLoadSnapshot = 1;
            }
            else if (argv[i][1] == 'P' && argv[i][2] == 'P' && argv[i][3] == ':')
            {
                sscanf(&argv[i][4], "%s", PreParamFile);
                GotPP = 1;
            }
            else if (argv[i][1] == 'S' && argv[i][2] == 'S' && argv[i][3] == ':')
            {
                sscanf(&argv[i][4], "%s", buf);
                fprintf(stderr, "### %s\n", buf);
                sep = strchr(buf, ',');
                if (!sep)
                    Perr = 1;
                else
                {
                    P.DoSaveSnapshot = 1;
                    *sep = ' ';
                    sscanf(buf, "%lf %s", &(P.SnapshotSaveTime), SnapshotSaveFile);
                }
            }
            else if (argv[i][1] == 'B' && argv[i][2] == 'M' && argv[i][3] == ':')
            {
                sscanf(&argv[i][4], "%s", buf);
                if (strcasecmp(buf, "png") == 0)
                {
#if defined(IMAGE_MAGICK) || defined(_WIN32)
                  P.BitmapFormat = BF_PNG;
#else
                  fprintf(stderr, "PNG Bitmaps not supported - please build with Image Magic or WIN32 support\n");
                  Perr = 1;
#endif
                }
                else if (strcasecmp(buf, "bmp") == 0)
                {
                  P.BitmapFormat = BF_BMP;
                }
                else
                {
                  fprintf(stderr, "Unrecognised bitmap format: %s\n", buf);
                  Perr = 1;
                }
            }
        }
        if (((GotS) && (GotL)) || (!GotP) || (!GotO)) Perr = 1;
    }

 
    sprintf(OutFile, "%s", OutFileBase);
 
    fprintf(stderr, "Param=%s\nOut=%s\nDens=%s\n", ParamFile, OutFile, DensityFile);
    fprintf(stderr, "Bitmap Format = *.%s\n", P.BitmapFormat == BF_PNG ? "png" : "bmp");
    if (Perr) ERR_CRITICAL_FMT("Syntax:\n%s /P:ParamFile /O:OutputFile [/AP:AirTravelFile] [/s:SchoolFile] [/D:DensityFile] [/L:NetworkFileToLoad | /S:NetworkFileToSave] [/R:R0scaling] SetupSeed1 SetupSeed2 RunSeed1 RunSeed2\n", argv[0]);

 
#ifdef _OPENMP
    P.NumThreads = omp_get_max_threads();
    if ((P.MaxNumThreads > 0) && (P.MaxNumThreads < P.NumThreads)) P.NumThreads = P.MaxNumThreads;
    if (P.NumThreads > MAX_NUM_THREADS)
    {
        fprintf(stderr, "Assigned number of threads (%d) > MAX_NUM_THREADS (%d)\n", P.NumThreads, MAX_NUM_THREADS);
        P.NumThreads = MAX_NUM_THREADS;
    }
    fprintf(stderr, "Using %d threads\n", P.NumThreads);
    omp_set_num_threads(P.NumThreads);
 
#pragma omp parallel default(shared)
    {
        fprintf(stderr, "Thread %i initialised\n", omp_get_thread_num());
    }
    /* fprintf(stderr,"int=%i\tfloat=%i\tdouble=%i\tint *=%i\n",(int) sizeof(int),(int) sizeof(float),(int) sizeof(double),(int) sizeof(int *));    */
#else
    P.NumThreads = 1;
#endif
    if (!GotPP)
    {
        sprintf(PreParamFile, ".." DIRECTORY_SEPARATOR "Pre_%s", ParamFile);
    }

 
 
    P.NumRealisations = GotNR;
    ReadParams(ParamFile, PreParamFile);
    if (GotScF) P.DoSchoolFile = 1;
    if (P.DoAirports)
    {
        if (!GotAP) ERR_CRITICAL_FMT("Syntax:\n%s /P:ParamFile /O:OutputFile /AP:AirTravelFile [/s:SchoolFile] [/D:DensityFile] [/L:NetworkFileToLoad | /S:NetworkFileToSave] [/R:R0scaling] SetupSeed1 SetupSeed2 RunSeed1 RunSeed2\n", argv[0]);
        ReadAirTravel(AirTravelFile);
    }


    SetupModel(DensityFile, NetworkFile, SchoolFile, RegDemogFile);
 
    for (i = 0; i < MAX_ADUNITS; i++) AdUnits[i].NI = 0;
    if (P.DoInterventionFile > 0)
        for (i = 0; i < P.DoInterventionFile; i++)
            ReadInterventions(InterventionFile[i]);
 
    fprintf(stderr, "Model setup in %lf seconds\n", ((double)(clock() - cl)) / CLOCKS_PER_SEC);
 
    //print out number of calls to random number generator

 
 
    P.NRactE = P.NRactNE = 0;
    for (i = 0; (i < P.NumRealisations) && (P.NRactNE < P.NumNonExtinctRealisations) ; i++)
    {
        if (P.NumRealisations > 1)
        {
            sprintf(OutFile, "%s.%i", OutFileBase, i);
            fprintf(stderr, "Realisation %i of %i  (time=%lf nr_ne=%i)\n", i + 1, P.NumRealisations,((double)(clock() - cl)) / CLOCKS_PER_SEC, P.NRactNE);
        }
        P.StopCalibration = P.ModelCalibIteration = 0;  // needed for calibration to work for multiple realisations
        P.PreControlClusterIdHolOffset = 0; // needed for calibration to work for multiple realisations
        P.PreControlClusterIdCaseThreshold = P.PreControlClusterIdCaseThreshold2; // needed for calibration to work for multiple realisations
        P.SeedingScaling = 1.0; // needed for calibration to work for multiple realisations
        if (i == 0 || (P.ResetSeeds && P.KeepSameSeeds))
        {
            P.nextRunSeed1 = P.runSeed1;
            P.nextRunSeed2 = P.runSeed2;
        }
        if (P.ResetSeeds) {
            //save these seeds to file
            SaveRandomSeeds();
        }
        // Now that we have set P.nextRunSeed* ready for the run, we need to save the values in case
        // we need to reinitialise the RNG after the run is interrupted.
        int32_t thisRunSeed1 = P.nextRunSeed1;
        int32_t thisRunSeed2 = P.nextRunSeed2;
//      if (i == 0 || P.ResetSeeds)
            setall(&P.nextRunSeed1, &P.nextRunSeed2);

        InitModel(i); //passing run number into RunModel so we can save run number in the infection event log: ggilani - 15/10/2014
        if (P.DoLoadSnapshot) LoadSnapshot();
        while (RunModel(i))
        {  // has been interrupted to reset holiday time. Note that this currently only happens in the first run, regardless of how many realisations are being run.
            int32_t tmp1 = thisRunSeed1;
            int32_t tmp2 = thisRunSeed2;
            setall(&tmp1, &tmp2);  // reset random number seeds to generate same run again after calibration.
            InitModel(i);
        }
        if (P.OutputNonSummaryResults)
        {
            if (((!TimeSeries[P.NumSamples - 1].extinct) || (!P.OutputOnlyNonExtinct)) && (P.OutputEveryRealisation))
            {
                SaveResults();
            }
        }
        if ((P.DoRecordInfEvents) && (P.RecordInfEventsPerRun == 1))
        {
            SaveEvents();
        }
    }
    sprintf(OutFile, "%s", OutFileBase);
 
    //Calculate origin destination matrix if needed
    if ((P.DoAdUnits) && (P.DoOriginDestinationMatrix))
    {
        CalcOriginDestMatrix_adunit();
        SaveOriginDestMatrix();
    }
 
    P.NRactual = P.NRactNE;
    TSMean = TSMeanNE; TSVar = TSVarNE;
    if ((P.DoRecordInfEvents) && (P.RecordInfEventsPerRun == 0))
    {
        SaveEvents();
    }
    sprintf(OutFile, "%s.avNE", OutFileBase);
    SaveSummaryResults();
    P.NRactual = P.NRactE;
    TSMean = TSMeanE; TSVar = TSVarE;
    sprintf(OutFile, "%s.avE", OutFileBase);
    //SaveSummaryResults();
 
    Bitmap_Finalise();
 
    fprintf(stderr, "Extinction in %i out of %i runs\n", P.NRactE, P.NRactNE + P.NRactE);
    fprintf(stderr, "Model ran in %lf seconds\n", ((double)(clock() - cl)) / CLOCKS_PER_SEC);
    fprintf(stderr, "Model finished\n");
}
 
 
void ReadParams(char* ParamFile, char* PreParamFile)
{
    FILE* ParamFile_dat, * PreParamFile_dat, * AdminFile_dat;
    double s, t, AgeSuscScale;
    int i, j, k, f, nc, na;
    char CountryNameBuf[128 * MAX_COUNTRIES], AdunitListNamesBuf[128 * MAX_ADUNITS];
 
    char* CountryNames[MAX_COUNTRIES];
    for (i = 0; i < MAX_COUNTRIES; i++) { CountryNames[i] = CountryNameBuf + 128 * i; CountryNames[i][0] = 0; }
    char* AdunitListNames[MAX_ADUNITS];
    for (i = 0; i < MAX_ADUNITS; i++) { AdunitListNames[i] = AdunitListNamesBuf + 128 * i; AdunitListNames[i][0] = 0; }
    if (!(ParamFile_dat = fopen(ParamFile, "rb"))) ERR_CRITICAL("Unable to open parameter file\n");
    PreParamFile_dat = fopen(PreParamFile, "rb");
    if (!(AdminFile_dat = fopen(AdunitFile, "rb"))) AdminFile_dat = ParamFile_dat;
    if (!GetInputParameter2(ParamFile_dat, AdminFile_dat, "Longitude cut line", "%lf", (void*)&(P.LongitudeCutLine), 1, 1, 0)) {
        P.LongitudeCutLine = -360.0;
    }
    AgeSuscScale = 1.0;
    GetInputParameter(ParamFile_dat, PreParamFile_dat, "Update timestep", "%lf", (void*)&(P.TimeStep), 1, 1, 0);
    GetInputParameter(ParamFile_dat, PreParamFile_dat, "Sampling timestep", "%lf", (void*)&(P.SampleStep), 1, 1, 0);
    if (P.TimeStep > P.SampleStep) ERR_CRITICAL("Update step must be smaller than sampling step\n");
    t = ceil(P.SampleStep / P.TimeStep - 1e-6);
    P.UpdatesPerSample = (int)t;
    P.TimeStep = P.SampleStep / t;
    P.TimeStepsPerDay = ceil(1.0 / P.TimeStep - 1e-6);
    fprintf(stderr, "Update step = %lf\nSampling step = %lf\nUpdates per sample=%i\nTimeStepsPerDay=%lf\n", P.TimeStep, P.SampleStep, P.UpdatesPerSample, P.TimeStepsPerDay);
    GetInputParameter(ParamFile_dat, PreParamFile_dat, "Sampling time", "%lf", (void*)&(P.SampleTime), 1, 1, 0);
    P.NumSamples = 1 + (int)ceil(P.SampleTime / P.SampleStep);
    GetInputParameter(PreParamFile_dat, AdminFile_dat, "Population size", "%i", (void*)&(P.PopSize), 1, 1, 0);
    if (P.NumRealisations == 0)
        {
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Number of realisations", "%i", (void*)&(P.NumRealisations), 1, 1, 0);
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of non-extinct realisations", "%i", (void*)&(P.NumNonExtinctRealisations), 1, 1, 0)) P.NumNonExtinctRealisations = P.NumRealisations;
        }
    else
        P.NumNonExtinctRealisations = P.NumRealisations;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of cases defining small outbreak", "%i", (void*) & (P.SmallEpidemicCases), 1, 1, 0)) P.SmallEpidemicCases = -1;
 
    P.NC = -1;
    GetInputParameter(ParamFile_dat, PreParamFile_dat, "Number of micro-cells per spatial cell width", "%i", (void*) & (P.NMCL), 1, 1, 0);
    //added parameter to reset seeds after every run
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Reset seeds for every run", "%i", (void*) & (P.ResetSeeds), 1, 1, 0)) P.ResetSeeds = 0;
    if (P.ResetSeeds)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Keep same seeds for every run", "%i", (void*) & (P.KeepSameSeeds), 1, 1, 0)) P.KeepSameSeeds = 0; //added this to control which seeds are used: ggilani 27/11/19
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Reset seeds after intervention", "%i", (void*) & (P.ResetSeedsPostIntervention), 1, 1, 0)) P.ResetSeedsPostIntervention = 0;
    if (P.ResetSeedsPostIntervention)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Time to reset seeds after intervention", "%i", (void*) & (P.TimeToResetSeeds), 1, 1, 0)) P.TimeToResetSeeds = 1000000;
    }
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Include households", "%i", (void*) & (P.DoHouseholds), 1, 1, 0)) P.DoHouseholds = 1;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputAge"                , "%i", (void*) & (P.OutputAge)                 , 1, 1, 0)) P.OutputAge = 1;                
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputSeverityAdminUnit"  , "%i", (void*) & (P.OutputSeverityAdminUnit)   , 1, 1, 0)) P.OutputSeverityAdminUnit = 1;  
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputSeverityAge"        , "%i", (void*) & (P.OutputSeverityAge)         , 1, 1, 0)) P.OutputSeverityAge = 1;        
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputR0"                 , "%i", (void*) & (P.OutputR0)                  , 1, 1, 0)) P.OutputR0 = 0;                 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputControls"           , "%i", (void*) & (P.OutputControls)            , 1, 1, 0)) P.OutputControls = 0;           
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputCountry"            , "%i", (void*) & (P.OutputCountry)             , 1, 1, 0)) P.OutputCountry = 0;            
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputAdUnitVar"          , "%i", (void*) & (P.OutputAdUnitVar)           , 1, 1, 0)) P.OutputAdUnitVar = 0;          
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputHousehold"          , "%i", (void*) & (P.OutputHousehold)           , 1, 1, 0)) P.OutputHousehold = 0;          
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputInfType"            , "%i", (void*) & (P.OutputInfType)             , 1, 1, 0)) P.OutputInfType = 0;            
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputNonSeverity"        , "%i", (void*) & (P.OutputNonSeverity)         , 1, 1, 0)) P.OutputNonSeverity = 0;        
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "OutputNonSummaryResults"  , "%i", (void*) & (P.OutputNonSummaryResults)   , 1, 1, 0)) P.OutputNonSummaryResults = 0;  
 
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel resolution", "%i", (void*)&P.NKR, 1, 1, 0)) P.NKR = 4000000;
    if (P.NKR < 2000000)
    {
        ERR_CRITICAL_FMT("[Kernel resolution] needs to be at least 2000000 - not %d", P.NKR);
    }
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel higher resolution factor", "%i", (void*)&P.NK_HR, 1, 1, 0)) P.NK_HR = P.NKR / 1600;
    if (P.NK_HR < 1 || P.NK_HR >= P.NKR)
    {
        ERR_CRITICAL_FMT("[Kernel higher resolution factor] needs to be in range [1, P.NKR = %d) - not %d", P.NKR, P.NK_HR);
    }
 
    if (P.DoHouseholds)
    {
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Household size distribution", "%lf", (void*)P.HouseholdSizeDistrib[0], MAX_HOUSEHOLD_SIZE, 1, 0);
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Household attack rate", "%lf", (void*) & (P.HouseholdTrans), 1, 1, 0);
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Household transmission denominator power", "%lf", (void*) & (P.HouseholdTransPow), 1, 1, 0);
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Correct age distribution after household allocation to exactly match specified demography", "%i", (void*)&(P.DoCorrectAgeDist), 1, 1, 0)) P.DoCorrectAgeDist = 0;
    }
    else
    {
        P.HouseholdTrans = 0.0;
        P.HouseholdTransPow = 1.0;
        P.HouseholdSizeDistrib[0][0] = 1.0;
        for (i = 1; i < MAX_HOUSEHOLD_SIZE; i++)
            P.HouseholdSizeDistrib[0][i] = 0;
    }
    for (i = 1; i < MAX_HOUSEHOLD_SIZE; i++)
        P.HouseholdSizeDistrib[0][i] = P.HouseholdSizeDistrib[0][i] + P.HouseholdSizeDistrib[0][i - 1];
    for (i = 0; i < MAX_HOUSEHOLD_SIZE; i++)
        P.HouseholdDenomLookup[i] = 1 / pow(((double)(i + 1)), P.HouseholdTransPow);
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Include administrative units within countries", "%i", (void*) & (P.DoAdUnits), 1, 1, 0)) P.DoAdUnits = 1;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Divisor for countries", "%i", (void*) & (P.CountryDivisor), 1, 1, 0)) P.CountryDivisor = 1;
    if (P.DoAdUnits)
    {
        char** AdunitNames, * AdunitNamesBuf;
        if (!(AdunitNames = (char**)malloc(3 * ADUNIT_LOOKUP_SIZE * sizeof(char*)))) ERR_CRITICAL("Unable to allocate temp storage\n");
        if (!(AdunitNamesBuf = (char*)malloc(3 * ADUNIT_LOOKUP_SIZE * 360 * sizeof(char)))) ERR_CRITICAL("Unable to allocate temp storage\n");
 
        for (i = 0; i < ADUNIT_LOOKUP_SIZE; i++)
        {
            P.AdunitLevel1Lookup[i] = -1;
            AdunitNames[3 * i] = AdunitNamesBuf + 3 * i * 360;
            AdunitNames[3 * i + 1] = AdunitNamesBuf + 3 * i * 360 + 60;
            AdunitNames[3 * i + 2] = AdunitNamesBuf + 3 * i * 360 + 160;
        }
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Divisor for level 1 administrative units", "%i", (void*)&(P.AdunitLevel1Divisor), 1, 1, 0)) P.AdunitLevel1Divisor = 1;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Mask for level 1 administrative units", "%i", (void*)&(P.AdunitLevel1Mask), 1, 1, 0)) P.AdunitLevel1Mask = 1000000000;
        na = (GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Codes and country/province names for admin units", "%s", (void*)AdunitNames, 3 * ADUNIT_LOOKUP_SIZE, 1, 0)) / 3;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Number of countries to include", "%i", (void*)&nc, 1, 1, 0)) nc = 0;
        if ((na > 0) && (nc>0))
        {
            P.DoAdunitBoundaries = (nc > 0);
            nc = abs(nc);
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "List of names of countries to include", "%s", (nc > 1) ? ((void*)CountryNames) : ((void*)CountryNames[0]), nc, 1, 0);
            P.NumAdunits = 0;
            for (i = 0; i < na; i++)
                for (j = 0; j < nc; j++)
                    if ((AdunitNames[3 * i + 1][0]) && (!strcmp(AdunitNames[3 * i + 1], CountryNames[j])) && (atoi(AdunitNames[3 * i]) != 0))
                    {
                        AdUnits[P.NumAdunits].id = atoi(AdunitNames[3 * i]);
                        P.AdunitLevel1Lookup[(AdUnits[P.NumAdunits].id % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor] = P.NumAdunits;
                        if (strlen(AdunitNames[3 * i + 1]) < 100) strcpy(AdUnits[P.NumAdunits].cnt_name, AdunitNames[3 * i + 1]);
                        if (strlen(AdunitNames[3 * i + 2]) < 200) strcpy(AdUnits[P.NumAdunits].ad_name, AdunitNames[3 * i + 2]);
                        //                      fprintf(stderr,"%i %s %s ## ",AdUnits[P.NumAdunits].id,AdUnits[P.NumAdunits].cnt_name,AdUnits[P.NumAdunits].ad_name);
                        P.NumAdunits++;
                    }
        }
        else
        {
            if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Number of level 1 administrative units to include", "%i", (void*) & (P.NumAdunits), 1, 1, 0)) P.NumAdunits = 0;
            if (P.NumAdunits > 0)
            {
                P.DoAdunitBoundaries = 1;
                if (P.NumAdunits > MAX_ADUNITS) ERR_CRITICAL("MAX_ADUNITS too small.\n");
                GetInputParameter(PreParamFile_dat, AdminFile_dat, "List of level 1 administrative units to include", "%s", (P.NumAdunits > 1) ? ((void*)AdunitListNames) : ((void*)AdunitListNames[0]), P.NumAdunits, 1, 0);
                na = P.NumAdunits;
                for (i = 0; i < P.NumAdunits; i++)
                {
                    f = 0;
                    if (na > 0)
                    {
                        for (j = 0; (j < na) && (!f); j++) f = (!strcmp(AdunitNames[3 * j + 2], AdunitListNames[i]));
                        if(f) k = atoi(AdunitNames[3 * (j-1)]);
                    }
                    if ((na == 0) || (!f)) k = atoi(AdunitListNames[i]);
                    AdUnits[i].id = k;
                    P.AdunitLevel1Lookup[(k % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor] = i;
                    for (j = 0; j < na; j++)
                        if (atoi(AdunitNames[3 * j]) == k)
                        {
                            if (strlen(AdunitNames[3 * j + 1]) < 100) strcpy(AdUnits[i].cnt_name, AdunitNames[3 * j + 1]);
                            if (strlen(AdunitNames[3 * j + 2]) < 200) strcpy(AdUnits[i].ad_name, AdunitNames[3 * j + 2]);
                            j = na;
                        }
                }
            }
            else
                P.DoAdunitBoundaries = 0;
        }
    free(AdunitNames);
    free(AdunitNamesBuf);
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output incidence by administrative unit", "%i", (void*) & (P.DoAdunitOutput), 1, 1, 0)) P.DoAdunitOutput = 0;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Draw administrative unit boundaries on maps", "%i", (void*) & (P.DoAdunitBoundaryOutput), 1, 1, 0)) P.DoAdunitBoundaryOutput = 0;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Correct administrative unit populations", "%i", (void*) & (P.DoCorrectAdunitPop), 1, 1, 0)) P.DoCorrectAdunitPop = 0;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Fix population size at specified value", "%i", (void*) & (P.DoSpecifyPop), 1, 1, 0)) P.DoSpecifyPop = 0;
        fprintf(stderr, "Using %i administrative units\n", P.NumAdunits);
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Divisor for administrative unit codes for boundary plotting on bitmaps", "%i", (void*) & (P.AdunitBitmapDivisor), 1, 1, 0)) P.AdunitBitmapDivisor = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Only output household to place distance distribution for one administrative unit", "%i", (void*) & (P.DoOutputPlaceDistForOneAdunit), 1, 1, 0)) P.DoOutputPlaceDistForOneAdunit = 0;
        if (P.DoOutputPlaceDistForOneAdunit)
        {
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Administrative unit for which household to place distance distribution to be output", "%i", (void*) & (P.OutputPlaceDistAdunit), 1, 1, 0)) P.DoOutputPlaceDistForOneAdunit = 0;
        }
    }
    else
    {
        P.DoAdunitBoundaries = P.DoAdunitBoundaryOutput = P.DoAdunitOutput = P.DoCorrectAdunitPop = P.DoSpecifyPop = 0;
        P.AdunitLevel1Divisor = 1; P.AdunitLevel1Mask = 1000000000;
        P.AdunitBitmapDivisor = P.AdunitLevel1Divisor;
    }
 
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Include age", "%i", (void*) & (P.DoAge), 1, 1, 0)) P.DoAge = 1;
    if (!P.DoAge)
    {
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            P.PropAgeGroup[0][i] = 1.0 / NUM_AGE_GROUPS;
        for (i = 0; i < NUM_AGE_GROUPS; i++)
        {
            P.InitialImmunity[i] = 0;
            P.AgeInfectiousness[i] = P.AgeSusceptibility[i] = 1;
            P.RelativeSpatialContact[i] = P.RelativeTravelRate[i] = 1.0;
        }
    }
    else
    {
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Initial immunity acts as partial immunity", "%i", (void*)&(P.DoPartialImmunity), 1, 1, 0)) P.DoPartialImmunity = 1;
        if ((P.DoHouseholds)&&(!P.DoPartialImmunity))
        {
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Initial immunity applied to all household members", "%i", (void*) & (P.DoWholeHouseholdImmunity), 1, 1, 0)) P.DoWholeHouseholdImmunity = 0;
        }
        else
            P.DoWholeHouseholdImmunity = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Initial immunity profile by age", "%lf", (void*)P.InitialImmunity, NUM_AGE_GROUPS, 1, 0))
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                P.InitialImmunity[i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rates by age", "%lf", (void*)P.RelativeSpatialContact, NUM_AGE_GROUPS, 1, 0))
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                P.RelativeSpatialContact[i] = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Age-dependent infectiousness", "%lf", (void*)P.AgeInfectiousness, NUM_AGE_GROUPS, 1, 0))
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                P.AgeInfectiousness[i] = 1.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Age-dependent susceptibility", "%lf", (void*)P.AgeSusceptibility, NUM_AGE_GROUPS, 1, 0))
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                P.AgeSusceptibility[i] = 1.0;
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Age distribution of population", "%lf", (void*)P.PropAgeGroup[0], NUM_AGE_GROUPS, 1, 0);
        t = 0;
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            t += P.PropAgeGroup[0][i];
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            P.PropAgeGroup[0][i] /= t;
        t = 0;
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            if (P.AgeSusceptibility[i] > t) t = P.AgeSusceptibility[i];  //peak susc has to be 1
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            P.AgeSusceptibility[i] /= t;
        AgeSuscScale = t;
        if (P.DoHouseholds) P.HouseholdTrans *= AgeSuscScale;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Relative travel rates by age", "%lf", (void*)P.RelativeTravelRate, NUM_AGE_GROUPS, 1, 0))
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                P.RelativeTravelRate[i] = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "WAIFW matrix", "%lf", (void*)P.WAIFW_Matrix, NUM_AGE_GROUPS, NUM_AGE_GROUPS, 0))
        {
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                for (j = 0; j < NUM_AGE_GROUPS; j++)
                    P.WAIFW_Matrix[i][j] = 1.0;
        }
        else
        {
            /* WAIFW matrix needs to be scaled to have max value of 1.
            1st index of matrix specifies host being infected, second the infector.
            Overall age variation in infectiousness/contact rates/susceptibility should be factored
            out of WAIFW_matrix and put in Age dep infectiousness/susceptibility for efficiency. */
            t = 0;
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                for (j = 0; j < NUM_AGE_GROUPS; j++)
                    if (P.WAIFW_Matrix[i][j] > t) t = P.WAIFW_Matrix[i][j];
            if (t > 0)
            {
                for (i = 0; i < NUM_AGE_GROUPS; i++)
                    for (j = 0; j < NUM_AGE_GROUPS; j++)
                        P.WAIFW_Matrix[i][j] /= t;
            }
            else
            {
                for (i = 0; i < NUM_AGE_GROUPS; i++)
                    for (j = 0; j < NUM_AGE_GROUPS; j++)
                        P.WAIFW_Matrix[i][j] = 1.0;
            }
        }
        P.DoDeath = 0;
        t = 0;
        for (i = 0; i < NUM_AGE_GROUPS; i++)    t += P.AgeInfectiousness[i] * P.PropAgeGroup[0][i];
        for (i = 0; i < NUM_AGE_GROUPS; i++)    P.AgeInfectiousness[i] /= t;
    }
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Include spatial transmission", "%i", (void*) & (P.DoSpatial), 1, 1, 0)) P.DoSpatial = 1;
    GetInputParameter(PreParamFile_dat, AdminFile_dat, "Kernel type", "%i", (void*) & (P.MoveKernelType), 1, 1, 0);
    GetInputParameter(PreParamFile_dat, AdminFile_dat, "Kernel scale", "%lf", (void*) & (P.MoveKernelScale), 1, 1, 0);
    if (P.KernelOffsetScale != 1)
    {
        P.MoveKernelScale *= P.KernelOffsetScale;
    }
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel 3rd param", "%lf", (void*) & (P.MoveKernelP3), 1, 1, 0)) P.MoveKernelP3 = 0;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel 4th param", "%lf", (void*) & (P.MoveKernelP4), 1, 1, 0)) P.MoveKernelP4 = 0;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel Shape", "%lf", (void*) & (P.MoveKernelShape), 1, 1, 0)) P.MoveKernelShape = 1.0;
    if (P.KernelPowerScale != 1)
    {
        P.MoveKernelShape *= P.KernelPowerScale;
    }
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Airport Kernel Type", "%i", (void*) & (P.AirportKernelType), 1, 1, 0)) P.AirportKernelType = P.MoveKernelType;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Airport Kernel Scale", "%lf", (void*) & (P.AirportKernelScale), 1, 1, 0)) P.AirportKernelScale = P.MoveKernelScale;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Airport Kernel Shape", "%lf", (void*) & (P.AirportKernelShape), 1, 1, 0)) P.AirportKernelShape = P.MoveKernelShape;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Airport Kernel 3rd param", "%lf", (void*) & (P.AirportKernelP3), 1, 1, 0)) P.AirportKernelP3 = P.MoveKernelP3;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Airport Kernel 4th param", "%lf", (void*) & (P.AirportKernelP4), 1, 1, 0)) P.AirportKernelP4 = P.MoveKernelP4;
 
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Include places", "%i", (void*)&(P.DoPlaces), 1, 1, 0)) P.DoPlaces = 1;
    if (P.DoPlaces)
    {
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Number of types of places", "%i", (void*)&(P.PlaceTypeNum), 1, 1, 0)) P.PlaceTypeNum = 0;
        if (P.PlaceTypeNum == 0) P.DoPlaces = P.DoAirports = 0;
    }
    else
        P.PlaceTypeNum = P.DoAirports = 0;
    if (P.DoPlaces)
    {
        if (P.PlaceTypeNum > NUM_PLACE_TYPES) ERR_CRITICAL("Too many place types\n");
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Minimum age for age group 1 in place types", "%i", (void*)P.PlaceTypeAgeMin, P.PlaceTypeNum, 1, 0);
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Maximum age for age group 1 in place types", "%i", (void*)P.PlaceTypeAgeMax, P.PlaceTypeNum, 1, 0);
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Proportion of age group 1 in place types", "%lf", (void*) & (P.PlaceTypePropAgeGroup), P.PlaceTypeNum, 1, 0);
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Proportion of age group 2 in place types", "%lf", (void*) & (P.PlaceTypePropAgeGroup2), P.PlaceTypeNum, 1, 0))
        {
            for (i = 0; i < NUM_PLACE_TYPES; i++)
            {
                P.PlaceTypePropAgeGroup2[i] = 0;
                P.PlaceTypeAgeMin2[i] = 0;
                P.PlaceTypeAgeMax2[i] = 1000;
            }
        }
        else
        {
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Minimum age for age group 2 in place types", "%i", (void*)P.PlaceTypeAgeMin2, P.PlaceTypeNum, 1, 0);
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Maximum age for age group 2 in place types", "%i", (void*)P.PlaceTypeAgeMax2, P.PlaceTypeNum, 1, 0);
        }
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Proportion of age group 3 in place types", "%lf", (void*) & (P.PlaceTypePropAgeGroup3), P.PlaceTypeNum, 1, 0))
        {
            for (i = 0; i < NUM_PLACE_TYPES; i++)
            {
                P.PlaceTypePropAgeGroup3[i] = 0;
                P.PlaceTypeAgeMin3[i] = 0;
                P.PlaceTypeAgeMax3[i] = 1000;
            }
        }
        else
        {
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Minimum age for age group 3 in place types", "%i", (void*)P.PlaceTypeAgeMin3, P.PlaceTypeNum, 1, 0);
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Maximum age for age group 3 in place types", "%i", (void*)P.PlaceTypeAgeMax3, P.PlaceTypeNum, 1, 0);
        }
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel shape params for place types", "%lf", (void*) & (P.PlaceTypeKernelShape), P.PlaceTypeNum, 1, 0))
        {
            for (i = 0; i < NUM_PLACE_TYPES; i++)
            {
                P.PlaceTypeKernelShape[i] = P.MoveKernelShape;
                P.PlaceTypeKernelScale[i] = P.MoveKernelScale;
            }
        }
        else
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Kernel scale params for place types", "%lf", (void*) & (P.PlaceTypeKernelScale), P.PlaceTypeNum, 1, 0);
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel 3rd param for place types", "%lf", (void*) & (P.PlaceTypeKernelP3), P.PlaceTypeNum, 1, 0))
        {
            for (i = 0; i < NUM_PLACE_TYPES; i++)
            {
                P.PlaceTypeKernelP3[i] = P.MoveKernelP3;
                P.PlaceTypeKernelP4[i] = P.MoveKernelP4;
            }
        }
        else
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Kernel 4th param for place types", "%lf", (void*) & (P.PlaceTypeKernelP4), P.PlaceTypeNum, 1, 0);
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Number of closest places people pick from (0=all) for place types", "%i", (void*) & (P.PlaceTypeNearestNeighb), P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++)
                P.PlaceTypeNearestNeighb[i] = 0;
        if (P.DoAdUnits)
        {
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Degree to which crossing administrative unit boundaries to go to places is inhibited", "%lf", (void*) & (P.InhibitInterAdunitPlaceAssignment), P.PlaceTypeNum, 1, 0))
                for (i = 0; i < NUM_PLACE_TYPES; i++)
                    P.InhibitInterAdunitPlaceAssignment[i] = 0;
        }
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Include air travel", "%i", (void*)&(P.DoAirports), 1, 1, 0)) P.DoAirports = 0;
        if (!P.DoAirports)
        {
            // Airports disabled => all places are not to do with airports, and we
            // have no hotels.
            P.PlaceTypeNoAirNum = P.PlaceTypeNum;
            P.HotelPlaceType = P.PlaceTypeNum;
        }
        else
        {
            // When airports are activated we must have at least one airport place
            // // and a hotel type.
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Number of non-airport places", "%i", (void*)&(P.PlaceTypeNoAirNum), 1, 1, 0);
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Hotel place type", "%i", (void*)&(P.HotelPlaceType), 1, 1, 0);
            if (P.PlaceTypeNoAirNum >= P.PlaceTypeNum) {
                ERR_CRITICAL_FMT("[Number of non-airport places] parameter (%d) is greater than number of places (%d).\n", P.PlaceTypeNoAirNum, P.PlaceTypeNum);
            }
            if (P.HotelPlaceType < P.PlaceTypeNoAirNum || P.HotelPlaceType >= P.PlaceTypeNum) {
                ERR_CRITICAL_FMT("[Hotel place type] parameter (%d) not in the range [%d, %d)\n", P.HotelPlaceType, P.PlaceTypeNoAirNum, P.PlaceTypeNum);
            }
 
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Scaling factor for input file to convert to daily traffic", "%lf", (void*) & (P.AirportTrafficScale), 1, 1, 0)) P.AirportTrafficScale = 1.0;
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of hotel attendees who are local", "%lf", (void*) & (P.HotelPropLocal), 1, 1, 0)) P.HotelPropLocal = 0;
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Distribution of duration of air journeys", "%lf", (void*) & (P.JourneyDurationDistrib), MAX_TRAVEL_TIME, 1, 0))
            {
                P.JourneyDurationDistrib[0] = 1;
                for (i = 0; i < MAX_TRAVEL_TIME; i++)
                    P.JourneyDurationDistrib[i] = 0;
            }
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Distribution of duration of local journeys", "%lf", (void*) & (P.LocalJourneyDurationDistrib), MAX_TRAVEL_TIME, 1, 0))
            {
                P.LocalJourneyDurationDistrib[0] = 1;
                for (i = 0; i < MAX_TRAVEL_TIME; i++)
                    P.LocalJourneyDurationDistrib[i] = 0;
            }
            P.MeanJourneyTime = P.MeanLocalJourneyTime = 0;
            for (i = 0; i < MAX_TRAVEL_TIME; i++)
            {
                P.MeanJourneyTime += ((double)(i)) * P.JourneyDurationDistrib[i];
                P.MeanLocalJourneyTime += ((double)(i)) * P.LocalJourneyDurationDistrib[i];
            }
            fprintf(stderr, "Mean duration of local journeys = %lf days\n", P.MeanLocalJourneyTime);
            for (i = 1; i < MAX_TRAVEL_TIME; i++)
            {
                P.JourneyDurationDistrib[i] += P.JourneyDurationDistrib[i - 1];
                P.LocalJourneyDurationDistrib[i] += P.LocalJourneyDurationDistrib[i - 1];
            }
            for (i = j = 0; i <= 1024; i++)
            {
                s = ((double)i) / 1024;
                while (P.JourneyDurationDistrib[j] < s)j++;
                P.InvJourneyDurationDistrib[i] = j;
            }
            for (i = j = 0; i <= 1024; i++)
            {
                s = ((double)i) / 1024;
                while (P.LocalJourneyDurationDistrib[j] < s)j++;
                P.InvLocalJourneyDurationDistrib[i] = j;
            }
        }
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Mean size of place types", "%lf", (void*)P.PlaceTypeMeanSize, P.PlaceTypeNum, 1, 0);
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Param 1 of place group size distribution", "%lf", (void*)P.PlaceTypeGroupSizeParam1, P.PlaceTypeNum, 1, 0);
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Power of place size distribution", "%lf", (void*)P.PlaceTypeSizePower, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++)
                P.PlaceTypeSizePower[i] = 0;
        //added to enable lognormal distribution - ggilani 09/02/17
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Standard deviation of place size distribution", "%lf", (void*)P.PlaceTypeSizeSD, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++)
                P.PlaceTypeSizeSD[i] = 0;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Offset of place size distribution", "%lf", (void*)P.PlaceTypeSizeOffset, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++)
                P.PlaceTypeSizeOffset[i] = 0;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Maximum of place size distribution", "%lf", (void*)P.PlaceTypeSizeMax, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++)
                P.PlaceTypeSizeMax[i] = 1e20;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Kernel type for place types", "%i", (void*)P.PlaceTypeKernelType, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++)
                P.PlaceTypeKernelType[i] = P.MoveKernelType;
        GetInputParameter(PreParamFile_dat, AdminFile_dat, "Place overlap matrix", "%lf", (void*)P.PlaceExclusivityMatrix, P.PlaceTypeNum * P.PlaceTypeNum, 1, 0); //changed from P.PlaceTypeNum,P.PlaceTypeNum,0);
/* Note P.PlaceExclusivityMatrix not used at present - places assumed exclusive (each person belongs to 0 or 1 place) */
 
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Proportion of between group place links", "%lf", (void*)P.PlaceTypePropBetweenGroupLinks, P.PlaceTypeNum, 1, 0);
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Relative transmission rates for place types", "%lf", (void*)P.PlaceTypeTrans, P.PlaceTypeNum, 1, 0);
        for (i = 0; i < P.PlaceTypeNum; i++) P.PlaceTypeTrans[i] *= AgeSuscScale;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Daily seasonality coefficients", "%lf", (void*)P.Seasonality, DAYS_PER_YEAR, 1, 0))
    {
        P.DoSeasonality = 0;
        for (i = 0; i < DAYS_PER_YEAR; i++)
            P.Seasonality[i] = 1;
    }
    else
    {
        P.DoSeasonality = 1;
        s = 0;
        for (i = 0; i < DAYS_PER_YEAR; i++)
            s += P.Seasonality[i];
        s += 1e-20;
        s /= DAYS_PER_YEAR;
        for (i = 0; i < DAYS_PER_YEAR; i++)
            P.Seasonality[i] /= s;
    }
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Number of seed locations", "%i", (void*) & (P.NumSeedLocations), 1, 1, 0)) P.NumSeedLocations = 1;
    if (P.NumSeedLocations > MAX_NUM_SEED_LOCATIONS)
    {
        fprintf(stderr, "Too many seed locations\n");
        P.NumSeedLocations = MAX_NUM_SEED_LOCATIONS;
    }
    GetInputParameter(PreParamFile_dat, AdminFile_dat, "Initial number of infecteds", "%i", (void*)P.NumInitialInfections, P.NumSeedLocations, 1, 0);
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Location of initial infecteds", "%lf", (void*)&(P.LocationInitialInfection[0][0]), P.NumSeedLocations * 2, 1, 0)) P.LocationInitialInfection[0][0] = P.LocationInitialInfection[0][1] = 0.0;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Minimum population in microcell of initial infection", "%i", (void*) & (P.MinPopDensForInitialInfection), 1, 1, 0)) P.MinPopDensForInitialInfection = 0;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Maximum population in microcell of initial infection", "%i", (void*)&(P.MaxPopDensForInitialInfection), 1, 1, 0)) P.MaxPopDensForInitialInfection = 10000000;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Randomise initial infection location", "%i", (void*) & (P.DoRandomInitialInfectionLoc), 1, 1, 0)) P.DoRandomInitialInfectionLoc=1;
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "All initial infections located in same microcell", "%i", (void*) & (P.DoAllInitialInfectioninSameLoc), 1, 1, 0)) P.DoAllInitialInfectioninSameLoc=0;
    if (P.DoAdUnits)
    {
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Administrative unit to seed initial infection into", "%s", (P.NumSeedLocations > 1) ? ((void*)AdunitListNames) : ((void*)AdunitListNames[0]), P.NumSeedLocations, 1, 0))
            for (i = 0; i < P.NumSeedLocations; i++) P.InitialInfectionsAdminUnit[i] = 0;
        else
            for (i = 0; i < P.NumSeedLocations; i++)
            {
                f = 0;
                if (P.NumAdunits > 0)
                {
                    for (j = 0; (j < P.NumAdunits) && (!f); j++) f = (!strcmp(AdUnits[j].ad_name, AdunitListNames[i]));
                    if (f) k = AdUnits[j-1].id;
                }
                if (!f) k = atoi(AdunitListNames[i]);
                P.InitialInfectionsAdminUnit[i] = k;
                P.InitialInfectionsAdminUnitId[i]=P.AdunitLevel1Lookup[(k % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor];
            }
        if(!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Administrative unit seeding weights", "%lf", (void*) & (P.InitialInfectionsAdminUnitWeight[0]), P.NumSeedLocations, 1, 0))
            for(i = 0; i < P.NumSeedLocations; i++) P.InitialInfectionsAdminUnitWeight[i] = 1.0;
        s=0;
        for(i = 0; i < P.NumSeedLocations; i++) s+=P.InitialInfectionsAdminUnitWeight[i];
        for(i = 0; i < P.NumSeedLocations; i++) P.InitialInfectionsAdminUnitWeight[i]/=s;
    //  for (i = 0; i < P.NumSeedLocations; i++) fprintf(stderr, "## %i %s %i %i %lf\n",i, AdUnits[P.InitialInfectionsAdminUnitId[i]].ad_name, P.InitialInfectionsAdminUnitId[i], P.InitialInfectionsAdminUnit[i], P.InitialInfectionsAdminUnitWeight[i]);
    }
    else
    {
        for (i = 0; i < P.NumSeedLocations; i++) P.InitialInfectionsAdminUnit[i] = 0;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Initial rate of importation of infections", "%lf", (void*)&(P.InfectionImportRate1), 1, 1, 0)) P.InfectionImportRate1 = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Changed rate of importation of infections", "%lf", (void*)&(P.InfectionImportRate2), 1, 1, 0)) P.InfectionImportRate2 = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Time when infection rate changes", "%lf", (void*)&(P.InfectionImportChangeTime), 1, 1, 0)) P.InfectionImportChangeTime = 1e10;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Imports via air travel", "%i", (void*)&(P.DoImportsViaAirports), 1, 1, 0)) P.DoImportsViaAirports = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Length of importation time profile provided", "%i", (void*)&(P.DurImportTimeProfile), 1, 1, 0)) P.DurImportTimeProfile = 0;
    if (P.DurImportTimeProfile > 0)
    {
        if (P.DurImportTimeProfile >= MAX_DUR_IMPORT_PROFILE) ERR_CRITICAL("MAX_DUR_IMPORT_PROFILE too small\n");
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Daily importation time profile", "%lf", (void*)P.ImportInfectionTimeProfile, P.DurImportTimeProfile, 1, 0);
    }
    GetInputParameter(ParamFile_dat, PreParamFile_dat, "Reproduction number", "%lf", (void*) & (P.R0), 1, 1, 0);
    GetInputParameter(ParamFile_dat, PreParamFile_dat, "Infectious period", "%lf", (void*) & (P.InfectiousPeriod), 1, 1, 0);
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "SD of individual variation in susceptibility", "%lf", (void*)&(P.SusceptibilitySD), 1, 1, 0)) P.SusceptibilitySD = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "SD of individual variation in infectiousness", "%lf", (void*) & (P.InfectiousnessSD), 1, 1, 0)) P.InfectiousnessSD = 0;
    if (GetInputParameter2(ParamFile_dat, PreParamFile_dat, "k of individual variation in infectiousness", "%lf", (void*)& s, 1, 1, 0)) P.InfectiousnessSD = 1.0 / sqrt(s);
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Model time varying infectiousness", "%i", (void*) & (P.DoInfectiousnessProfile), 1, 1, 0)) P.DoInfectiousnessProfile = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Power of scaling of spatial R0 with density", "%lf", (void*) & (P.R0DensityScalePower), 1, 1, 0)) P.R0DensityScalePower = 0;
    if (P.DoInfectiousnessProfile)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Infectiousness profile", "%lf", (void*)P.infectious_prof, INFPROF_RES, 1, 0))
        {
            for (i = 0; i < INFPROF_RES; i++)
                P.infectious_prof[i] = 1;
        }
        k = (int)ceil(P.InfectiousPeriod / P.TimeStep);
        if (k >= MAX_INFECTIOUS_STEPS) ERR_CRITICAL("MAX_INFECTIOUS_STEPS not big enough\n");
        s = 0;
        P.infectious_prof[INFPROF_RES] = 0;
        for (i = 0; i < MAX_INFECTIOUS_STEPS; i++)  P.infectiousness[i] = 0;
        for (i = 0; i < k; i++)
        {
            t = (((double)i) * P.TimeStep / P.InfectiousPeriod * INFPROF_RES);
            j = (int)t;
            t -= (double)j;
            if (j < INFPROF_RES)
                s += (P.infectiousness[i] = P.infectious_prof[j] * (1 - t) + P.infectious_prof[j + 1] * t);
            else
                s += (P.infectiousness[i] = P.infectious_prof[INFPROF_RES]);
        }
        s /= ((double)k);
        for (i = 0; i <= k; i++) P.infectiousness[i] /= s;
        for (i = 0; i <= CDF_RES; i++) P.infectious_icdf[i] = exp(-1.0);
    }
    else
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Infectious period inverse CDF", "%lf", (void*)P.infectious_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.infectious_icdf, ICDF_START);
        }
        k = (int)ceil(P.InfectiousPeriod * P.infectious_icdf[CDF_RES] / P.TimeStep);
        if (k >= MAX_INFECTIOUS_STEPS) ERR_CRITICAL("MAX_INFECTIOUS_STEPS not big enough\n");
        for (i = 0; i < k; i++) P.infectiousness[i] = 1.0;
        P.infectiousness[k] = 0;
        for (i = 0; i <= CDF_RES; i++) P.infectious_icdf[i] = exp(-P.infectious_icdf[i]);
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Include latent period", "%i", (void*) & (P.DoLatent), 1, 1, 0)) P.DoLatent = 0;
    if (P.DoLatent)
    {
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Latent period", "%lf", (void*) & (P.LatentPeriod), 1, 1, 0);
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Latent period inverse CDF", "%lf", (void*)P.latent_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.latent_icdf, 1e10);
        }
        for (i = 0; i <= CDF_RES; i++)
            P.latent_icdf[i] = exp(-P.latent_icdf[i]);
    }
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Include symptoms", "%i", (void*) & (P.DoSymptoms), 1, 1, 0)) P.DoSymptoms = 0;
    if (!P.DoSymptoms)
    {
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            P.ProportionSymptomatic[i] = 0;
        P.FalsePositiveRate = 0;
        P.SymptInfectiousness = 1.0;
        P.LatentToSymptDelay = 0;
    }
    else
    {
        if (P.DoAge)
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Proportion symptomatic by age group", "%lf", (void*)P.ProportionSymptomatic, NUM_AGE_GROUPS, 1, 0);
        else
        {
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Proportion symptomatic", "%lf", (void*)P.ProportionSymptomatic, 1, 1, 0);
            for (i = 1; i < NUM_AGE_GROUPS; i++)
                P.ProportionSymptomatic[i] = P.ProportionSymptomatic[0];
        }
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Delay from end of latent period to start of symptoms", "%lf", (void*) & (P.LatentToSymptDelay), 1, 1, 0);
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Relative rate of random contacts if symptomatic", "%lf", (void*) & (P.SymptSpatialContactRate), 1, 1, 0);
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Symptomatic infectiousness relative to asymptomatic", "%lf", (void*) & (P.SymptInfectiousness), 1, 1, 0);
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Model symptomatic withdrawal to home as true absenteeism", "%i", (void*)& P.DoRealSymptWithdrawal, 1, 1, 0)) P.DoRealSymptWithdrawal = 0;
        if (P.DoPlaces)
        {
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Relative level of place attendance if symptomatic", "%lf", (void*)P.SymptPlaceTypeContactRate, P.PlaceTypeNum, 1, 0);
            if (P.DoRealSymptWithdrawal)
            {
                for (j = 0; j < NUM_PLACE_TYPES; j++)
                {
                    P.SymptPlaceTypeWithdrawalProp[j] = 1.0 - P.SymptPlaceTypeContactRate[j];
                    P.SymptPlaceTypeContactRate[j] = 1.0;
                }
            }
            else
                for (j = 0; j < NUM_PLACE_TYPES; j++) P.SymptPlaceTypeWithdrawalProp[j] = 0.0;
        }
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum age of child at home for whom one adult also stays at home", "%i", (void*)& P.CaseAbsentChildAgeCutoff, 1, 1, 0)) P.CaseAbsentChildAgeCutoff = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of children at home for whom one adult also stays at home", "%lf", (void*)& P.CaseAbsentChildPropAdultCarers, 1, 1, 0)) P.CaseAbsentChildPropAdultCarers = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place close round household", "%i", (void*)&P.PlaceCloseRoundHousehold, 1, 1, 0)) P.PlaceCloseRoundHousehold = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Absenteeism place closure", "%i", (void*)&P.AbsenteeismPlaceClosure, 1, 1, 0)) P.AbsenteeismPlaceClosure = 0;
        if (P.AbsenteeismPlaceClosure)
        {
            P.CaseAbsenteeismDelay = 0;  // Set to zero for tracking absenteeism
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max absent time", "%i", (void*)&P.MaxAbsentTime, 1, 1, 0)) P.MaxAbsentTime = MAX_ABSENT_TIME;
            if (P.MaxAbsentTime > MAX_ABSENT_TIME || P.MaxAbsentTime < 0)
            {
                ERR_CRITICAL_FMT("[Max absent time] out of range (%d), should be in range [0, %d]", P.MaxAbsentTime, MAX_ABSENT_TIME);
            }
        }
        else
        {
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay in starting place absenteeism for cases who withdraw", "%lf", (void*)& P.CaseAbsenteeismDelay, 1, 1, 0)) P.CaseAbsenteeismDelay = 0;
            P.MaxAbsentTime = 0; // Not used when !P.AbsenteeismPlaceClosure
        }
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of place absenteeism for cases who withdraw", "%lf", (void*)& P.CaseAbsenteeismDuration, 1, 1, 0)) P.CaseAbsenteeismDuration = 7;
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "False positive rate", "%lf", (void*) & (P.FalsePositiveRate), 1, 1, 0)) P.FalsePositiveRate = 0.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "False positive per capita incidence", "%lf", (void*) & (P.FalsePositivePerCapitaIncidence), 1, 1, 0)) P.FalsePositivePerCapitaIncidence = 0.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "False positive relative incidence by age", "%lf", (void*)P.FalsePositiveAgeRate, NUM_AGE_GROUPS, 1, 0))
            for (j = 0; j < NUM_AGE_GROUPS; j++) P.FalsePositiveAgeRate[j] = 1.0;
    }
 
    if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Do Severity Analysis", "%i", (void*) & (P.DoSeverity), 1, 1, 0)) P.DoSeverity = 0;
    if(P.DoSeverity == 1)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "MeanTimeToTest", "%lf", (void*)&(P.Mean_TimeToTest), 1, 1, 0)) P.Mean_TimeToTest = 0.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "MeanTimeToTestOffset", "%lf", (void*)&(P.Mean_TimeToTestOffset), 1, 1, 0)) P.Mean_TimeToTestOffset = 1.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "MeanTimeToTestCriticalOffset", "%lf", (void*)&(P.Mean_TimeToTestCriticalOffset), 1, 1, 0)) P.Mean_TimeToTestCriticalOffset = 1.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "MeanTimeToTestCritRecovOffset", "%lf", (void*)&(P.Mean_TimeToTestCritRecovOffset), 1, 1, 0)) P.Mean_TimeToTestCritRecovOffset = 1.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Age dependent severity delays", "%i", (void*)&i, 1, 1, 0)) i = 0;
        if (!i)
        {
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_MildToRecovery", "%lf", (void*)&(P.Mean_MildToRecovery[0]), 1, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_ILIToRecovery", "%lf", (void*)&(P.Mean_ILIToRecovery[0]), 1, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_SARIToRecovery", "%lf", (void*)&(P.Mean_SARIToRecovery[0]), 1, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_CriticalToCritRecov", "%lf", (void*)&(P.Mean_CriticalToCritRecov[0]), 1, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_CritRecovToRecov", "%lf", (void*)&(P.Mean_CritRecovToRecov[0]), 1, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_ILIToSARI", "%lf", (void*)&(P.Mean_ILIToSARI[0]), 1, 1, 0);
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Mean_ILIToDeath", "%lf", (void*)&(P.Mean_ILIToDeath[0]), 1, 1, 0)) P.Mean_ILIToDeath[0] = 7.0;
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_SARIToCritical", "%lf", (void*)&(P.Mean_SARIToCritical[0]), 1, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_SARIToDeath", "%lf", (void*)&(P.Mean_SARIToDeath[0]), 1, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_CriticalToDeath", "%lf", (void*)&(P.Mean_CriticalToDeath[0]), 1, 1, 0);
            for (j = 1; j < NUM_AGE_GROUPS; j++)
            {
                P.Mean_MildToRecovery[j] = P.Mean_MildToRecovery[0];
                P.Mean_ILIToRecovery[j] = P.Mean_ILIToRecovery[0];
                P.Mean_SARIToRecovery[j] = P.Mean_SARIToRecovery[0];
                P.Mean_CriticalToCritRecov[j] = P.Mean_CriticalToCritRecov[0];
                P.Mean_CritRecovToRecov[j] = P.Mean_CritRecovToRecov[0];
                P.Mean_ILIToSARI[j] = P.Mean_ILIToSARI[0];
                P.Mean_ILIToDeath[j] = P.Mean_ILIToDeath[0];
                P.Mean_SARIToCritical[j] = P.Mean_SARIToCritical[0];
                P.Mean_SARIToDeath[j] = P.Mean_SARIToDeath[0];
                P.Mean_CriticalToDeath[j] = P.Mean_CriticalToDeath[0];
            }
        }
        else
        {
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_MildToRecovery", "%lf", (void*)(P.Mean_MildToRecovery), NUM_AGE_GROUPS, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_ILIToRecovery", "%lf", (void*)(P.Mean_ILIToRecovery), NUM_AGE_GROUPS, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_SARIToRecovery", "%lf", (void*)(P.Mean_SARIToRecovery), NUM_AGE_GROUPS, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_CriticalToCritRecov", "%lf", (void*)(P.Mean_CriticalToCritRecov), NUM_AGE_GROUPS, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_CritRecovToRecov", "%lf", (void*)(P.Mean_CritRecovToRecov), NUM_AGE_GROUPS, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_ILIToSARI", "%lf", (void*)(P.Mean_ILIToSARI), NUM_AGE_GROUPS, 1, 0);
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Mean_ILIToDeath", "%lf", (void*)(P.Mean_ILIToDeath), NUM_AGE_GROUPS, 1, 0))
                for (j = 0; j < NUM_AGE_GROUPS; j++) P.Mean_ILIToDeath[j] = 7.0;
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_SARIToCritical", "%lf", (void*)(P.Mean_SARIToCritical), NUM_AGE_GROUPS, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_SARIToDeath", "%lf", (void*)(P.Mean_SARIToDeath), NUM_AGE_GROUPS, 1, 0);
            GetInputParameter(ParamFile_dat, PreParamFile_dat, "Mean_CriticalToDeath", "%lf", (void*)(P.Mean_CriticalToDeath), NUM_AGE_GROUPS, 1, 0);
        }
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "MildToRecovery_icdf", "%lf", (void*)P.MildToRecovery_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.MildToRecovery_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.MildToRecovery_icdf[i] = exp(-P.MildToRecovery_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "ILIToRecovery_icdf", "%lf", (void*)P.ILIToRecovery_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.ILIToRecovery_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.ILIToRecovery_icdf[i] = exp(-P.ILIToRecovery_icdf[i]);
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "ILIToDeath_icdf", "%lf", (void*)P.ILIToDeath_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.ILIToDeath_icdf, ICDF_START);
        }
        for (i = 0; i <= CDF_RES; i++) P.ILIToDeath_icdf[i] = exp(-P.ILIToDeath_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "SARIToRecovery_icdf", "%lf", (void*)P.SARIToRecovery_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.SARIToRecovery_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.SARIToRecovery_icdf[i] = exp(-P.SARIToRecovery_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "CriticalToCritRecov_icdf", "%lf", (void*)P.CriticalToCritRecov_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.CriticalToCritRecov_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.CriticalToCritRecov_icdf[i] = exp(-P.CriticalToCritRecov_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "CritRecovToRecov_icdf", "%lf", (void*)P.CritRecovToRecov_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.CritRecovToRecov_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.CritRecovToRecov_icdf[i] = exp(-P.CritRecovToRecov_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "ILIToSARI_icdf", "%lf", (void*)P.ILIToSARI_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.ILIToSARI_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.ILIToSARI_icdf[i] = exp(-P.ILIToSARI_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "SARIToCritical_icdf", "%lf", (void*)P.SARIToCritical_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.SARIToCritical_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.SARIToCritical_icdf[i] = exp(-P.SARIToCritical_icdf[i]);
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "SARIToDeath_icdf"     , "%lf", (void*)P.SARIToDeath_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.SARIToDeath_icdf, ICDF_START);
        }
        for (i = 0; i <= CDF_RES; i++) P.SARIToDeath_icdf[i] = exp(-P.SARIToDeath_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "CriticalToDeath_icdf", "%lf", (void*)P.CriticalToDeath_icdf, CDF_RES + 1, 1, 0))
        {
            SetICDF(P.CriticalToDeath_icdf, ICDF_START);
        }
        for(i = 0; i <= CDF_RES; i++) P.CriticalToDeath_icdf[i] = exp(-P.CriticalToDeath_icdf[i]);
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Prop_Mild_ByAge", "%lf", (void*)P.Prop_Mild_ByAge, NUM_AGE_GROUPS, 1, 0))
            for(i = 0; i < NUM_AGE_GROUPS; i++)
                P.Prop_Mild_ByAge[i] = 0.5;
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Prop_ILI_ByAge", "%lf", (void*)P.Prop_ILI_ByAge, NUM_AGE_GROUPS, 1, 0))
            for(i = 0; i < NUM_AGE_GROUPS; i++)
                P.Prop_ILI_ByAge[i] = 0.3;
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Prop_SARI_ByAge", "%lf", (void*)P.Prop_SARI_ByAge, NUM_AGE_GROUPS, 1, 0))
            for(i = 0; i < NUM_AGE_GROUPS; i++)
                P.Prop_SARI_ByAge[i] = 0.15;
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Prop_Critical_ByAge", "%lf", (void*)P.Prop_Critical_ByAge, NUM_AGE_GROUPS, 1, 0))
            for(i = 0; i < NUM_AGE_GROUPS; i++)
                P.Prop_Critical_ByAge[i] = 0.05;
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "CFR_SARI_ByAge", "%lf", (void*)P.CFR_SARI_ByAge, NUM_AGE_GROUPS, 1, 0))
            for(i = 0; i < NUM_AGE_GROUPS; i++)
                P.CFR_SARI_ByAge[i] = 0.50;
 
        if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "CFR_Critical_ByAge", "%lf", (void*)P.CFR_Critical_ByAge, NUM_AGE_GROUPS, 1, 0))
            for(i = 0; i < NUM_AGE_GROUPS; i++)
                P.CFR_Critical_ByAge[i] = 0.50;
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "CFR_ILI_ByAge", "%lf", (void*)P.CFR_ILI_ByAge, NUM_AGE_GROUPS, 1, 0))
            for (i = 0; i < NUM_AGE_GROUPS; i++)
                P.CFR_ILI_ByAge[i] = 0.00;
    }
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bounding box for bitmap", "%lf", (void*) & (P.BoundingBox[0]), 4, 1, 0))
    {
        P.BoundingBox[0] = P.BoundingBox[1] = 0.0;
        P.BoundingBox[2] = P.BoundingBox[3] = 1.0;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Spatial domain for simulation", "%lf", (void*) & (P.SpatialBoundingBox[0]), 4, 1, 0))
    {
        P.SpatialBoundingBox[0] = P.SpatialBoundingBox[1] = 0.0;
        P.SpatialBoundingBox[2] = P.SpatialBoundingBox[3] = 1.0;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Grid size", "%lf", (void*) & (P.in_cells_.width_), 1, 1, 0)) P.in_cells_.width_ = 1.0 / 120.0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Use long/lat coord system", "%i", (void*) & (P.DoUTM_coords), 1, 1, 0)) P.DoUTM_coords = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bitmap scale", "%lf", (void*) & (P.BitmapScale), 1, 1, 0)) P.BitmapScale = 1.0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bitmap y:x aspect scaling", "%lf", (void*) & (P.BitmapAspectScale), 1, 1, 0)) P.BitmapAspectScale = 1.0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Bitmap movie frame interval", "%i", (void*) & (P.BitmapMovieFrame), 1, 1, 0)) P.BitmapMovieFrame = 250;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output bitmap", "%i", (void*) & (P.OutputBitmap), 1, 1, 0)) P.OutputBitmap = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output bitmap detected", "%i", (void*) & (P.OutputBitmapDetected), 1, 1, 0)) P.OutputBitmapDetected = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output immunity on bitmap", "%i", (void*) & (P.DoImmuneBitmap), 1, 1, 0)) P.DoImmuneBitmap = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output infection tree", "%i", (void*) & (P.DoInfectionTree), 1, 1, 0)) P.DoInfectionTree = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Do one generation", "%i", (void*) & (P.DoOneGen), 1, 1, 0)) P.DoOneGen = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output every realisation", "%i", (void*) & (P.OutputEveryRealisation), 1, 1, 0)) P.OutputEveryRealisation = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number to sample for correlations", "%i", (void*) & (P.MaxCorrSample), 1, 1, 0)) P.MaxCorrSample = 1000000000;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Assume SI model", "%i", (void*) & (P.DoSI), 1, 1, 0)) P.DoSI = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Assume periodic boundary conditions", "%i", (void*) & (P.DoPeriodicBoundaries), 1, 1, 0)) P.DoPeriodicBoundaries = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Only output non-extinct realisations", "%i", (void*) & (P.OutputOnlyNonExtinct), 1, 1, 0)) P.OutputOnlyNonExtinct = 0;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Use cases per thousand threshold for area controls", "%i", (void*) & (P.DoPerCapitaTriggers), 1, 1, 0)) P.DoPerCapitaTriggers = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Use global triggers for interventions", "%i", (void*) & (P.DoGlobalTriggers), 1, 1, 0)) P.DoGlobalTriggers = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Use admin unit triggers for interventions", "%i", (void*) & (P.DoAdminTriggers), 1, 1, 0)) P.DoAdminTriggers = 0;
    if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Use ICU case triggers for interventions", "%i", (void*) & (P.DoICUTriggers), 1, 1, 0)) P.DoICUTriggers = 0;
    if (P.DoGlobalTriggers)  P.DoAdminTriggers = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Divisor for per-capita area threshold (default 1000)", "%i", (void*) & (P.IncThreshPop), 1, 1, 0)) P.IncThreshPop = 1000;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Divisor for per-capita global threshold (default 1000)", "%i", (void*) & (P.GlobalIncThreshPop), 1, 1, 0)) P.GlobalIncThreshPop = 1000;
 
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of sampling intervals over which cumulative incidence measured for global trigger", "%i", (void*) & (P.TriggersSamplingInterval), 1, 1, 0)) P.TriggersSamplingInterval = 10000000;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of cases detected for treatment", "%lf", (void*) & (P.PostAlertControlPropCasesId), 1, 1, 0)) P.PostAlertControlPropCasesId = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of cases detected before outbreak alert", "%lf", (void*) & (P.PreAlertControlPropCasesId), 1, 1, 0)) P.PreAlertControlPropCasesId = 1.0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger alert on deaths", "%i", (void*)&(P.PreControlClusterIdUseDeaths), 1, 1, 0)) P.PreControlClusterIdUseDeaths = 0;
    if (P.PreControlClusterIdUseDeaths)
    {
        if (P.PreControlClusterIdCaseThreshold == 0)
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of deaths accummulated before alert", "%i", (void*)&(P.PreControlClusterIdCaseThreshold), 1, 1, 0)) P.PreControlClusterIdCaseThreshold = 0;
    }
    else if (P.PreControlClusterIdCaseThreshold == 0)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of detected cases needed before outbreak alert triggered", "%i", (void*) & (P.PreControlClusterIdCaseThreshold), 1, 1, 0)) P.PreControlClusterIdCaseThreshold = 0;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Alert trigger starts after interventions", "%i", (void*)&(P.DoAlertTriggerAfterInterv), 1, 1, 0)) P.DoAlertTriggerAfterInterv = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Day of year trigger is reached", "%lf", (void*)&(P.PreControlClusterIdCalTime), 1, 1, 0)) P.PreControlClusterIdCalTime = -1;
    if (P.DoAlertTriggerAfterInterv)
    {
        GetInputParameter(ParamFile_dat, PreParamFile_dat, "Day of year interventions start", "%lf", (void*)&(P.PreIntervIdCalTime), 1, 1, 0);
        if (P.PreControlClusterIdCalTime <= P.PreIntervIdCalTime)
            P.DoAlertTriggerAfterInterv = 0;
        else
        {
            P.AlertTriggerAfterIntervThreshold = P.PreControlClusterIdCaseThreshold;
            P.PreControlClusterIdCaseThreshold = 1000;
        }
    }
    else
        P.PreIntervIdCalTime = P.PreControlClusterIdCalTime;
    P.PreControlClusterIdCaseThreshold2 = P.PreControlClusterIdCaseThreshold;
    //if (P.DoAlertTriggerAfterInterv) P.ResetSeeds =P.KeepSameSeeds = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of days to accummulate cases/deaths before alert", "%i", (void*)&(P.PreControlClusterIdDuration), 1, 1, 0)) P.PreControlClusterIdDuration = 1000;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Only use confirmed cases to trigger alert", "%i", (void*) & (P.DoEarlyCaseDiagnosis), 1, 1, 0)) P.DoEarlyCaseDiagnosis = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Only treat mixing groups within places", "%i", (void*) & (P.DoPlaceGroupTreat), 1, 1, 0)) P.DoPlaceGroupTreat = 0;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Treatment trigger incidence per cell"             , "%lf", (void*) & (P.TreatCellIncThresh)           , 1, 1, 0)) P.TreatCellIncThresh            = 1000000000;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Case isolation trigger incidence per cell"        , "%lf", (void*) & (P.CaseIsolation_CellIncThresh)  , 1, 1, 0)) P.CaseIsolation_CellIncThresh   = P.TreatCellIncThresh;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Household quarantine trigger incidence per cell"  , "%lf", (void*) & (P.HHQuar_CellIncThresh)         , 1, 1, 0)) P.HHQuar_CellIncThresh          = P.TreatCellIncThresh;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative susceptibility of treated individual", "%lf", (void*) & (P.TreatSuscDrop), 1, 1, 0)) P.TreatSuscDrop = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative infectiousness of treated individual", "%lf", (void*) & (P.TreatInfDrop), 1, 1, 0)) P.TreatInfDrop = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of symptomatic cases resulting in death prevented by treatment", "%lf", (void*) & (P.TreatDeathDrop), 1, 1, 0)) P.TreatDeathDrop = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of symptomatic cases prevented by treatment", "%lf", (void*) & (P.TreatSympDrop), 1, 1, 0)) P.TreatSympDrop = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to treat cell", "%lf", (void*) & (P.TreatDelayMean), 1, 1, 0)) P.TreatDelayMean = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of course of treatment", "%lf", (void*) & (P.TreatCaseCourseLength), 1, 1, 0)) P.TreatCaseCourseLength = 5;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of course of prophylaxis", "%lf", (void*) & (P.TreatProphCourseLength), 1, 1, 0)) P.TreatProphCourseLength = 10;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of detected cases treated", "%lf", (void*) & (P.TreatPropCases), 1, 1, 0)) P.TreatPropCases = 1;
    if (P.DoHouseholds)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of households of cases treated", "%lf", (void*) & (P.TreatPropCaseHouseholds), 1, 1, 0)) P.TreatPropCaseHouseholds = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of household prophylaxis policy", "%lf", (void*) & (P.TreatHouseholdsDuration), 1, 1, 0)) P.TreatHouseholdsDuration = USHRT_MAX / P.TimeStepsPerDay;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion treated", "%lf", (void*) & (P.TreatPropRadial), 1, 1, 0)) P.TreatPropRadial = 1.0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion treated in radial prophylaxis", "%lf", (void*) & (P.TreatPropRadial), 1, 1, 0)) P.TreatPropRadial = 1.0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Treatment radius", "%lf", (void*) & (P.TreatRadius), 1, 1, 0)) P.TreatRadius = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of place/geographic prophylaxis policy", "%lf", (void*) & (P.TreatPlaceGeogDuration), 1, 1, 0)) P.TreatPlaceGeogDuration = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Treatment start time", "%lf", (void*) & (P.TreatTimeStartBase), 1, 1, 0)) P.TreatTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
    if (P.DoPlaces)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of places treated after case detected", "%lf", (void*)P.TreatPlaceProbCaseId, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.TreatPlaceProbCaseId[i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of people treated in targeted places", "%lf", (void*)P.TreatPlaceTotalProp, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.TreatPlaceTotalProp[i] = 0;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of doses available", "%lf", (void*) & (P.TreatMaxCoursesBase), 1, 1, 0)) P.TreatMaxCoursesBase = 1e20;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Start time of additional treatment production", "%lf", (void*) & (P.TreatNewCoursesStartTime), 1, 1, 0)) P.TreatNewCoursesStartTime = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Rate of additional treatment production (courses per day)", "%lf", (void*) & (P.TreatNewCoursesRate), 1, 1, 0)) P.TreatNewCoursesRate = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of people targeted with radial prophylaxis per case", "%i", (void*) & (P.TreatMaxCoursesPerCase), 1, 1, 0)) P.TreatMaxCoursesPerCase = 1000000000;
 
 
    if (P.DoAdUnits)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Treat administrative units rather than rings", "%i", (void*) & (P.TreatByAdminUnit), 1, 1, 0)) P.TreatByAdminUnit = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Administrative unit divisor for treatment", "%i", (void*) & (P.TreatAdminUnitDivisor), 1, 1, 0)) P.TreatAdminUnitDivisor = 1;
        if ((P.TreatAdminUnitDivisor == 0) || (P.TreatByAdminUnit == 0)) { P.TreatByAdminUnit = 0; P.TreatAdminUnitDivisor = 1; }
    }
    else
    {
        P.TreatAdminUnitDivisor = 1; P.TreatByAdminUnit = 0;
    }
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Vaccination trigger incidence per cell", "%lf", (void*) & (P.VaccCellIncThresh), 1, 1, 0)) P.VaccCellIncThresh = 1000000000;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative susceptibility of vaccinated individual", "%lf", (void*) & (P.VaccSuscDrop), 1, 1, 0)) P.VaccSuscDrop = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative susceptibility of individual vaccinated after switch time", "%lf", (void*) & (P.VaccSuscDrop2), 1, 1, 0)) P.VaccSuscDrop2 = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Switch time at which vaccine efficacy increases", "%lf", (void*) & (P.VaccTimeEfficacySwitch), 1, 1, 0)) P.VaccTimeEfficacySwitch = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Decay rate of vaccine efficacy (per year)", "%lf", (void*) & (P.VaccEfficacyDecay), 1, 1, 0)) P.VaccEfficacyDecay = 0;
    P.VaccEfficacyDecay /= DAYS_PER_YEAR;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative infectiousness of vaccinated individual", "%lf", (void*) & (P.VaccInfDrop), 1, 1, 0)) P.VaccInfDrop = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of symptomatic cases resulting in death prevented by vaccination", "%lf", (void*) & (P.VaccMortDrop), 1, 1, 0)) P.VaccMortDrop = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of symptomatic cases prevented by vaccination", "%lf", (void*) & (P.VaccSympDrop), 1, 1, 0)) P.VaccSympDrop = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to vaccinate", "%lf", (void*) & (P.VaccDelayMean), 1, 1, 0)) P.VaccDelayMean = 0;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay from vaccination to full protection", "%lf", (void*) & (P.VaccTimeToEfficacy), 1, 1, 0)) P.VaccTimeToEfficacy = 0;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Years between rounds of vaccination", "%lf", (void*) & (P.VaccCampaignInterval), 1, 1, 0)) P.VaccCampaignInterval = 1e10;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max vaccine doses per day", "%i", (void*) & (P.VaccDosePerDay), 1, 1, 0)) P.VaccDosePerDay = -1;
    P.VaccCampaignInterval *= DAYS_PER_YEAR;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of rounds of vaccination", "%i", (void*) & (P.VaccMaxRounds), 1, 1, 0)) P.VaccMaxRounds = 1;
    if (P.DoHouseholds)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of households of cases vaccinated", "%lf", (void*) & (P.VaccPropCaseHouseholds), 1, 1, 0)) P.VaccPropCaseHouseholds = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of household vaccination policy", "%lf", (void*) & (P.VaccHouseholdsDuration), 1, 1, 0)) P.VaccHouseholdsDuration = USHRT_MAX / P.TimeStepsPerDay;
    }
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Vaccination start time", "%lf", (void*) & (P.VaccTimeStartBase), 1, 1, 0)) P.VaccTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of population vaccinated", "%lf", (void*) & (P.VaccProp), 1, 1, 0)) P.VaccProp = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Time taken to reach max vaccination coverage (in years)", "%lf", (void*) & (P.VaccCoverageIncreasePeriod), 1, 1, 0)) P.VaccCoverageIncreasePeriod = 0;
    P.VaccCoverageIncreasePeriod *= DAYS_PER_YEAR;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Time to start geographic vaccination", "%lf", (void*) & (P.VaccTimeStartGeo), 1, 1, 0)) P.VaccTimeStartGeo = 1e10;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Vaccination radius", "%lf", (void*) & (P.VaccRadius), 1, 1, 0)) P.VaccRadius = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Minimum radius from case to vaccinate", "%lf", (void*) & (P.VaccMinRadius), 1, 1, 0)) P.VaccMinRadius = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of vaccine courses available", "%lf", (void*) & (P.VaccMaxCoursesBase), 1, 1, 0)) P.VaccMaxCoursesBase = 1e20;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Start time of additional vaccine production", "%lf", (void*) & (P.VaccNewCoursesStartTime), 1, 1, 0)) P.VaccNewCoursesStartTime = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "End time of additional vaccine production", "%lf", (void*) & (P.VaccNewCoursesEndTime), 1, 1, 0)) P.VaccNewCoursesEndTime = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Rate of additional vaccine production (courses per day)", "%lf", (void*) & (P.VaccNewCoursesRate), 1, 1, 0)) P.VaccNewCoursesRate = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Apply mass rather than reactive vaccination", "%i", (void*) & (P.DoMassVacc), 1, 1, 0)) P.DoMassVacc = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Priority age range for mass vaccination", "%i", (void*)P.VaccPriorityGroupAge, 2, 1, 0)) { P.VaccPriorityGroupAge[0] = 1; P.VaccPriorityGroupAge[1] = 0; }
    if (P.DoAdUnits)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Vaccinate administrative units rather than rings", "%i", (void*) & (P.VaccByAdminUnit), 1, 1, 0)) P.VaccByAdminUnit = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Administrative unit divisor for vaccination", "%i", (void*) & (P.VaccAdminUnitDivisor), 1, 1, 0)) P.VaccAdminUnitDivisor = 1;
        if ((P.VaccAdminUnitDivisor == 0) || (P.VaccByAdminUnit == 0)) P.VaccAdminUnitDivisor = 1;
    }
    else
    {
        P.VaccAdminUnitDivisor = 1; P.VaccByAdminUnit = 0;
    }
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Movement restrictions trigger incidence per cell", "%i", (void*) & (P.MoveRestrCellIncThresh), 1, 1, 0)) P.MoveRestrCellIncThresh = 1000000000;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to start movement restrictions", "%lf", (void*) & (P.MoveDelayMean), 1, 1, 0)) P.MoveDelayMean = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of movement restrictions", "%lf", (void*) & (P.MoveRestrDuration), 1, 1, 0)) P.MoveRestrDuration = 7;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual movements after restrictions", "%lf", (void*) & (P.MoveRestrEffect), 1, 1, 0)) P.MoveRestrEffect = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Minimum radius of movement restrictions", "%lf", (void*) & (P.MoveRestrRadius), 1, 1, 0)) P.MoveRestrRadius = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Movement restrictions start time", "%lf", (void*) & (P.MoveRestrTimeStartBase), 1, 1, 0)) P.MoveRestrTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Impose blanket movement restrictions", "%i", (void*) & (P.DoBlanketMoveRestr), 1, 1, 0)) P.DoBlanketMoveRestr = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Movement restrictions only once", "%i", (void*) & (P.DoMoveRestrOnceOnly), 1, 1, 0)) P.DoMoveRestrOnceOnly = 0;
    if (P.DoMoveRestrOnceOnly) P.DoMoveRestrOnceOnly = 4;
    if (P.DoAdUnits)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Movement restrictions in administrative units rather than rings", "%i", (void*) & (P.MoveRestrByAdminUnit), 1, 1, 0)) P.MoveRestrByAdminUnit = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Administrative unit divisor for movement restrictions", "%i", (void*) & (P.MoveRestrAdminUnitDivisor), 1, 1, 0)) P.MoveRestrAdminUnitDivisor = 1;
        if ((P.MoveRestrAdminUnitDivisor == 0) || (P.MoveRestrByAdminUnit == 0)) P.MoveRestrAdminUnitDivisor = 1;
    }
    else
    {
        P.MoveRestrAdminUnitDivisor = 1; P.MoveRestrByAdminUnit = 0;
    }
 
    //Intervention delays and durations by admin unit: ggilani 16/03/20
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Include intervention delays by admin unit", "%i", (void*) & (P.DoInterventionDelaysByAdUnit), 1, 1, 0)) P.DoInterventionDelaysByAdUnit = 0;
    if (P.DoInterventionDelaysByAdUnit)
    {
        //Set up arrays to temporarily store parameters per admin unit
        double AdunitDelayToSocialDistance  [MAX_ADUNITS];
        double AdunitDelayToHQuarantine     [MAX_ADUNITS];
        double AdunitDelayToCaseIsolation   [MAX_ADUNITS];
        double AdunitDelayToPlaceClose      [MAX_ADUNITS];
        double AdunitDurationSocialDistance [MAX_ADUNITS];
        double AdunitDurationHQuarantine    [MAX_ADUNITS];
        double AdunitDurationCaseIsolation  [MAX_ADUNITS];
        double AdunitDurationPlaceClose     [MAX_ADUNITS];
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to social distancing by admin unit"         , "%lf", (void*)AdunitDelayToSocialDistance , P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDelayToSocialDistance   [i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to household quarantine by admin unit"      , "%lf", (void*)AdunitDelayToHQuarantine    , P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDelayToHQuarantine      [i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to case isolation by admin unit"            , "%lf", (void*)AdunitDelayToCaseIsolation  , P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDelayToCaseIsolation    [i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to place closure by admin unit"             , "%lf", (void*)AdunitDelayToPlaceClose     , P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDelayToPlaceClose       [i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of social distancing by admin unit"      , "%lf", (void*)AdunitDurationSocialDistance, P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDurationSocialDistance  [i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of household quarantine by admin unit"   , "%lf", (void*)AdunitDurationHQuarantine   , P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDurationHQuarantine     [i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of case isolation by admin unit"         , "%lf", (void*)AdunitDurationCaseIsolation , P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDurationCaseIsolation   [i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of place closure by admin unit"          , "%lf", (void*)AdunitDurationPlaceClose    , P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDurationPlaceClose      [i] = 0;
 
        for (i = 0; i < P.NumAdunits; i++)
        {
            AdUnits[i].SocialDistanceDelay          = AdunitDelayToSocialDistance   [i];
            AdUnits[i].SocialDistanceDuration       = AdunitDurationSocialDistance  [i];
            AdUnits[i].HQuarantineDelay             = AdunitDelayToHQuarantine      [i];
            AdUnits[i].HQuarantineDuration          = AdunitDurationHQuarantine     [i];
            AdUnits[i].CaseIsolationDelay           = AdunitDelayToCaseIsolation    [i];
            AdUnits[i].CaseIsolationPolicyDuration  = AdunitDurationCaseIsolation   [i];
            AdUnits[i].PlaceCloseDelay              = AdunitDelayToPlaceClose       [i];
            AdUnits[i].PlaceCloseDuration           = AdunitDurationPlaceClose      [i];
        }
    }

 
    //New code for digital contact tracing - ggilani: 09/03/20
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Include digital contact tracing", "%i", (void*) & (P.DoDigitalContactTracing), 1, 1, 0)) P.DoDigitalContactTracing = 0;
    if (P.DoDigitalContactTracing)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Digital contact tracing trigger incidence per cell", "%lf", (void*) & (P.DigitalContactTracing_CellIncThresh), 1, 1, 0)) P.DigitalContactTracing_CellIncThresh = 1000000000;
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of population or households covered by digital contact tracing", "%lf", (void*) & (P.PropPopUsingDigitalContactTracing), 1, 1, 0)) P.PropPopUsingDigitalContactTracing = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of smartphone users by age", "%lf", (void*)P.ProportionSmartphoneUsersByAge, NUM_AGE_GROUPS, 1, 0))
        {
            for (i = 0; i < NUM_AGE_GROUPS; i++)
            {
                P.ProportionSmartphoneUsersByAge[i] = 1;
            }
        }
        if (P.DoPlaces)
        {
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Cluster digital app clusters by household", "%i", (void*) & (P.ClusterDigitalContactUsers), 1, 1, 0)) P.ClusterDigitalContactUsers = 0; // by default, don't cluster by location
        }
        else
        {
            P.ClusterDigitalContactUsers = 0;
        }
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of digital contacts who self-isolate", "%lf", (void*) & (P.ProportionDigitalContactsIsolate), 1, 1, 0)) P.ProportionDigitalContactsIsolate = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of contacts to trace per index case", "%i", (void*)&(P.MaxDigitalContactsToTrace), 1, 1, 0)) P.MaxDigitalContactsToTrace = MAX_CONTACTS;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay between isolation of index case and contacts", "%lf", (void*) & (P.DigitalContactTracingDelay), 1, 1, 0)) P.DigitalContactTracingDelay = P.TimeStep;
        //we really need one timestep between to make sure contact is not processed before index
        if (P.DigitalContactTracingDelay == 0) P.DigitalContactTracingDelay = P.TimeStep;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Length of self-isolation for digital contacts", "%lf", (void*) & (P.LengthDigitalContactIsolation), 1, 1, 0)) P.LengthDigitalContactIsolation = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Spatial scaling factor - digital contact tracing", "%lf", (void*) & (P.ScalingFactorSpatialDigitalContacts), 1, 1, 0)) P.ScalingFactorSpatialDigitalContacts = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place scaling factor - digital contact tracing", "%lf", (void*)&(P.ScalingFactorPlaceDigitalContacts), 1, 1, 0)) P.ScalingFactorPlaceDigitalContacts = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Digital contact tracing start time", "%lf", (void*) & (P.DigitalContactTracingTimeStartBase), 1, 1, 0)) P.DigitalContactTracingTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of digital contact tracing policy", "%lf", (void*) & (P.DigitalContactTracingPolicyDuration), 1, 1, 0)) P.DigitalContactTracingPolicyDuration = 7;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output digital contact tracing", "%i", (void*) & (P.OutputDigitalContactTracing), 1, 1, 0)) P.OutputDigitalContactTracing = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output digital contact distribution", "%i", (void*)&(P.OutputDigitalContactDist), 1, 1, 0)) P.OutputDigitalContactDist = 0;
 
        //if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Include household contacts in digital contact tracing", "%i", (void*) & (P.IncludeHouseholdDigitalContactTracing), 1, 1, 0)) P.IncludeHouseholdDigitalContactTracing = 1;
        //if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Include place group contacts in digital contact tracing", "%i", (void*) & (P.IncludePlaceGroupDigitalContactTracing), 1, 1, 0)) P.IncludePlaceGroupDigitalContactTracing = 1;
 
        //added admin unit specific delays by admin unit
        if (P.DoInterventionDelaysByAdUnit)
        {
            double AdunitDelayToDCT[MAX_ADUNITS];
            double AdunitDurationDCT[MAX_ADUNITS];
 
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to digital contact tracing by admin unit", "%lf", (void*)AdunitDelayToDCT, P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDelayToDCT[i] = 0;
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of digital contact tracing by admin unit", "%lf", (void*)AdunitDurationDCT, P.NumAdunits, 1, 0)) for (i = 0; i < P.NumAdunits; i++) AdunitDurationDCT[i] = 0;
            for (i = 0; i < P.NumAdunits; i++)
            {
                AdUnits[i].DCTDelay = AdunitDelayToDCT[i];
                AdUnits[i].DCTDuration = AdunitDurationDCT[i];
            }
        }
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Isolate index cases in digital contact tracing", "%i", (void*)&(P.DCTIsolateIndexCases), 1, 1, 0)) P.DCTIsolateIndexCases = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual contacts after digital contact tracing isolation", "%lf", (void*)&(P.DCTCaseIsolationEffectiveness), 1, 1, 0)) P.DCTCaseIsolationEffectiveness = P.CaseIsolationEffectiveness;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual household contacts after digital contact tracing isolation", "%lf", (void*)&(P.DCTCaseIsolationHouseEffectiveness), 1, 1, 0)) P.DCTCaseIsolationHouseEffectiveness = P.CaseIsolationHouseEffectiveness;
        //initialise total number of users to 0
        P.NDigitalContactUsers = 0;
        P.NDigitalHouseholdUsers = 0;
 
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay between symptom onset and isolation for index case", "%lf", (void*)&(P.DelayFromIndexCaseDetectionToDCTIsolation), 1, 1, 0)) P.DelayFromIndexCaseDetectionToDCTIsolation = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Test index cases and contacts", "%i", (void*)&(P.DoDCTTest), 1, 1, 0)) P.DoDCTTest = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to test index case", "%lf", (void*)&(P.DelayToTestIndexCase), 1, 1, 0)) P.DelayToTestIndexCase = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to test DCT contacts", "%lf", (void*)&(P.DelayToTestDCTContacts), 1, 1, 0)) P.DelayToTestDCTContacts = 7;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Testing specificity - DCT", "%lf", (void*)&(P.SpecificityDCT), 1, 1, 0)) P.SpecificityDCT = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Testing sensitivity - DCT", "%lf", (void*)&(P.SensitivityDCT), 1, 1, 0)) P.SensitivityDCT = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Find contacts of digital contacts", "%i", (void*)&(P.FindContactsOfDCTContacts), 1, 1, 0)) P.FindContactsOfDCTContacts = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Remove contacts of a negative index case", "%i", (void*)&(P.RemoveContactsOfNegativeIndexCase), 1, 1, 0)) P.RemoveContactsOfNegativeIndexCase = 0;
    }
    else
    {
        //Set these to 1 so it doesn't interfere with code if we aren't using digital contact tracing.
 
        P.ScalingFactorSpatialDigitalContacts = 1;
        P.ScalingFactorPlaceDigitalContacts = 1;
    }

 
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for place closure", "%i", (void*) & (P.PlaceCloseCellIncThresh1), 1, 1, 0)) P.PlaceCloseCellIncThresh1 = 1000000000;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for second place closure", "%i", (void*)&(P.PlaceCloseCellIncThresh2), 1, 1, 0)) P.PlaceCloseCellIncThresh2 = 1000000000;
    if (P.PlaceCloseCellIncThresh1 < 0) P.PlaceCloseCellIncThresh1 = 1000000000;
    if (P.PlaceCloseCellIncThresh2 < 0) P.PlaceCloseCellIncThresh2 = 1000000000;
    if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for end of place closure", "%i", (void*) & (P.PlaceCloseCellIncStopThresh), 1, 1, 0)) P.PlaceCloseCellIncStopThresh = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to start place closure", "%lf", (void*) & (P.PlaceCloseDelayMean), 1, 1, 0)) P.PlaceCloseDelayMean = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of place closure", "%lf", (void*) & (P.PlaceCloseDurationBase), 1, 1, 0)) P.PlaceCloseDurationBase = 7;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of second place closure", "%lf", (void*) & (P.PlaceCloseDuration2), 1, 1, 0)) P.PlaceCloseDuration2 = 7;
    if (P.DoPlaces)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of places remaining open after closure by place type", "%lf", (void*)P.PlaceCloseEffect, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.PlaceCloseEffect[i] = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportional attendance after closure by place type", "%lf", (void*)P.PlaceClosePropAttending, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.PlaceClosePropAttending[i] = 0;
    }
    if (P.DoHouseholds)
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rate after closure", "%lf", (void*)& P.PlaceCloseHouseholdRelContact, 1, 1, 0)) P.PlaceCloseHouseholdRelContact = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rate after closure", "%lf", (void*)& P.PlaceCloseSpatialRelContact, 1, 1, 0)) P.PlaceCloseSpatialRelContact = 1;
 
    if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Include holidays", "%i", (void*) & (P.DoHolidays), 1, 1, 0)) P.DoHolidays = 0;
    if (P.DoHolidays)
    {
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Proportion of places remaining open during holidays by place type", "%lf", (void*)P.HolidayEffect, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.HolidayEffect[i] = 1;
        if (!GetInputParameter2(PreParamFile_dat, AdminFile_dat, "Number of holidays", "%i", (void*) & (P.NumHolidays), 1, 1, 0)) P.NumHolidays = 0;
        if (P.NumHolidays > DAYS_PER_YEAR) P.NumHolidays = DAYS_PER_YEAR;
        if (P.NumHolidays > 0)
        {
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Holiday start times", "%lf", (void*)P.HolidayStartTime, P.NumHolidays, 1, 0);
            GetInputParameter(PreParamFile_dat, AdminFile_dat, "Holiday durations", "%lf", (void*)P.HolidayDuration, P.NumHolidays, 1, 0);
        }
    }
    else
        P.NumHolidays = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Minimum radius for place closure", "%lf", (void*) & (P.PlaceCloseRadius), 1, 1, 0)) P.PlaceCloseRadius = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure start time", "%lf", (void*) & (P.PlaceCloseTimeStartBase), 1, 1, 0)) P.PlaceCloseTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure second start time", "%lf", (void*) & (P.PlaceCloseTimeStartBase2), 1, 1, 0)) P.PlaceCloseTimeStartBase2 = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Places close only once", "%i", (void*) & (P.DoPlaceCloseOnceOnly), 1, 1, 0)) P.DoPlaceCloseOnceOnly = 0;
    if (P.DoPlaceCloseOnceOnly) P.DoPlaceCloseOnceOnly = 4;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure incidence threshold", "%i", (void*) & (P.PlaceCloseIncTrig1), 1, 1, 0)) P.PlaceCloseIncTrig1 = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure second incidence threshold", "%i", (void*)&(P.PlaceCloseIncTrig2), 1, 1, 0)) P.PlaceCloseIncTrig2 = P.PlaceCloseIncTrig1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure fractional incidence threshold", "%lf", (void*) & (P.PlaceCloseFracIncTrig), 1, 1, 0)) P.PlaceCloseFracIncTrig = 0;
    if ((P.DoAdUnits) && (P.DoPlaces))
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure in administrative units rather than rings", "%i", (void*) & (P.PlaceCloseByAdminUnit), 1, 1, 0)) P.PlaceCloseByAdminUnit = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Administrative unit divisor for place closure", "%i", (void*) & (P.PlaceCloseAdminUnitDivisor), 1, 1, 0)) P.PlaceCloseAdminUnitDivisor = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place types to close for admin unit closure (0/1 array)", "%i", (void*) & (P.PlaceCloseAdunitPlaceTypes), P.PlaceTypeNum, 1, 0))
            for (i = 0; i < P.PlaceTypeNum; i++) P.PlaceCloseAdunitPlaceTypes[i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Cumulative proportion of place members needing to become sick for admin unit closure", "%lf", (void*) & (P.PlaceCloseCasePropThresh), 1, 1, 0)) P.PlaceCloseCasePropThresh = 2;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of places in admin unit needing to pass threshold for place closure", "%lf", (void*) & (P.PlaceCloseAdunitPropThresh), 1, 1, 0)) P.PlaceCloseAdunitPropThresh = 2;
        if ((P.PlaceCloseAdminUnitDivisor < 1) || (P.PlaceCloseByAdminUnit == 0)) P.PlaceCloseAdminUnitDivisor = 1;
    }
    else
    {
        P.PlaceCloseAdminUnitDivisor = 1; P.PlaceCloseByAdminUnit = 0;
    }

 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for social distancing", "%i", (void*) & (P.SocDistCellIncThresh), 1, 1, 0)) P.SocDistCellIncThresh = 1000000000;
    if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for end of social distancing", "%i", (void*) & (P.SocDistCellIncStopThresh), 1, 1, 0)) P.SocDistCellIncStopThresh = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of social distancing", "%lf", (void*) & (P.SocDistDuration), 1, 1, 0)) P.SocDistDuration = 7;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of social distancing after change", "%lf", (void*) & (P.SocDistDuration2), 1, 1, 0)) P.SocDistDuration2 = 7;
    if (P.DoPlaces)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative place contact rate given social distancing by place type", "%lf", (void*)P.SocDistPlaceEffect, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.SocDistPlaceEffect[i] = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative place contact rate given enhanced social distancing by place type", "%lf", (void*)P.EnhancedSocDistPlaceEffect, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.EnhancedSocDistPlaceEffect[i] = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative place contact rate given social distancing by place type after change", "%lf", (void*)P.SocDistPlaceEffect2, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.SocDistPlaceEffect2[i] = P.SocDistPlaceEffect[i];
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative place contact rate given enhanced social distancing by place type after change", "%lf", (void*)P.EnhancedSocDistPlaceEffect2, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.EnhancedSocDistPlaceEffect2[i] = P.EnhancedSocDistPlaceEffect[i];
    }
    if (P.DoHouseholds)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rate given social distancing", "%lf", (void*)&P.SocDistHouseholdEffect, 1, 1, 0)) P.SocDistHouseholdEffect = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rate given enhanced social distancing", "%lf", (void*)&P.EnhancedSocDistHouseholdEffect, 1, 1, 0)) P.EnhancedSocDistHouseholdEffect = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rate given social distancing  after change", "%lf", (void*)&P.SocDistHouseholdEffect2, 1, 1, 0)) P.SocDistHouseholdEffect2 = P.SocDistHouseholdEffect;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rate given enhanced social distancing after change", "%lf", (void*)&P.EnhancedSocDistHouseholdEffect2, 1, 1, 0)) P.EnhancedSocDistHouseholdEffect2 = P.EnhancedSocDistHouseholdEffect;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Cluster compliance with enhanced social distancing by household", "%i", (void*)&P.EnhancedSocDistClusterByHousehold, 1, 1, 0)) P.EnhancedSocDistClusterByHousehold = 0;
    }
    else
        P.EnhancedSocDistClusterByHousehold = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rate given social distancing", "%lf", (void*)& P.SocDistSpatialEffect, 1, 1, 0)) P.SocDistSpatialEffect = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rate given social distancing after change", "%lf", (void*)&P.SocDistSpatialEffect2, 1, 1, 0)) P.SocDistSpatialEffect2 = P.SocDistSpatialEffect;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Minimum radius for social distancing", "%lf", (void*) & (P.SocDistRadius), 1, 1, 0)) P.SocDistRadius = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Social distancing start time", "%lf", (void*) & (P.SocDistTimeStartBase), 1, 1, 0)) P.SocDistTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay for change in effectiveness of social distancing", "%lf", (void*)&(P.SocDistChangeDelay), 1, 1, 0)) P.SocDistChangeDelay = USHRT_MAX / P.TimeStepsPerDay;
    if(!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion compliant with enhanced social distancing by age group", "%lf", (void*)P.EnhancedSocDistProportionCompliant, NUM_AGE_GROUPS, 1, 0))
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion compliant with enhanced social distancing", "%lf", (void*)&t, 1, 1, 0)) t = 0;
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            P.EnhancedSocDistProportionCompliant[i] = t;
    }
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rate given enhanced social distancing", "%lf", (void*)& P.EnhancedSocDistSpatialEffect, 1, 1, 0)) P.EnhancedSocDistSpatialEffect = 1;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rate given enhanced social distancing after change", "%lf", (void*)&P.EnhancedSocDistSpatialEffect2, 1, 1, 0)) P.EnhancedSocDistSpatialEffect2 = P.EnhancedSocDistSpatialEffect;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Social distancing only once", "%i", (void*) & (P.DoSocDistOnceOnly), 1, 1, 0)) P.DoSocDistOnceOnly = 0;
    if (P.DoSocDistOnceOnly) P.DoSocDistOnceOnly = 4;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Airport closure effectiveness", "%lf", (void*) & (P.AirportCloseEffectiveness), 1, 1, 0)) P.AirportCloseEffectiveness = 0;
    P.AirportCloseEffectiveness = 1.0 - P.AirportCloseEffectiveness;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Airport closure start time", "%lf", (void*) & (P.AirportCloseTimeStartBase), 1, 1, 0)) P.AirportCloseTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Airport closure duration", "%lf", (void*) & (P.AirportCloseDuration), 1, 1, 0)) P.AirportCloseDuration = USHRT_MAX / P.TimeStepsPerDay;

 
    if (P.DoHouseholds)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Retrigger household quarantine with each new case in quarantine window", "%i", (void*) & (P.DoHQretrigger), 1, 1, 0)) P.DoHQretrigger =0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Household quarantine start time", "%lf", (void*) & (P.HQuarantineTimeStartBase), 1, 1, 0)) P.HQuarantineTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to start household quarantine", "%lf", (void*) & (P.HQuarantineDelay), 1, 1, 0)) P.HQuarantineDelay = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Length of time households are quarantined", "%lf", (void*) & (P.HQuarantineHouseDuration), 1, 1, 0)) P.HQuarantineHouseDuration = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of household quarantine policy", "%lf", (void*) & (P.HQuarantinePolicyDuration), 1, 1, 0)) P.HQuarantinePolicyDuration = USHRT_MAX / P.TimeStepsPerDay;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rate after quarantine", "%lf", (void*) & (P.HQuarantineHouseEffect), 1, 1, 0)) P.HQuarantineHouseEffect = 1;
        if (P.DoPlaces)
        {
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual place contacts after household quarantine by place type", "%lf", (void*)P.HQuarantinePlaceEffect, P.PlaceTypeNum, 1, 0))
                for (i = 0; i < NUM_PLACE_TYPES; i++) P.HQuarantinePlaceEffect[i] = 1;
        }
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual spatial contacts after household quarantine", "%lf", (void*) & (P.HQuarantineSpatialEffect), 1, 1, 0)) P.HQuarantineSpatialEffect = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Household level compliance with quarantine", "%lf", (void*) & (P.HQuarantinePropHouseCompliant), 1, 1, 0)) P.HQuarantinePropHouseCompliant = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Individual level compliance with quarantine", "%lf", (void*) & (P.HQuarantinePropIndivCompliant), 1, 1, 0)) P.HQuarantinePropIndivCompliant = 1;
    }
    else
        P.HQuarantineTimeStartBase = 1e10;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Case isolation start time", "%lf", (void*) & (P.CaseIsolationTimeStartBase), 1, 1, 0)) P.CaseIsolationTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of detected cases isolated", "%lf", (void*) & (P.CaseIsolationProp), 1, 1, 0)) P.CaseIsolationProp = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Delay to start case isolation", "%lf", (void*) & (P.CaseIsolationDelay), 1, 1, 0)) P.CaseIsolationDelay = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of case isolation", "%lf", (void*) & (P.CaseIsolationDuration), 1, 1, 0)) P.CaseIsolationDuration = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of case isolation policy", "%lf", (void*) & (P.CaseIsolationPolicyDuration), 1, 1, 0)) P.CaseIsolationPolicyDuration = 1e10;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual contacts after case isolation", "%lf", (void*) & (P.CaseIsolationEffectiveness), 1, 1, 0)) P.CaseIsolationEffectiveness = 1;
    if (P.DoHouseholds)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual household contacts after case isolation", "%lf", (void*) & (P.CaseIsolationHouseEffectiveness), 1, 1, 0))
            P.CaseIsolationHouseEffectiveness = P.CaseIsolationEffectiveness;
    }

 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Vary efficacies over time", "%i", (void*) & (P.VaryEfficaciesOverTime), 1, 1, 0)) P.VaryEfficaciesOverTime = 0;
    if (!P.VaryEfficaciesOverTime)
    {
        P.Num_SD_ChangeTimes = 1;
        P.Num_CI_ChangeTimes = 1;
        P.Num_HQ_ChangeTimes = 1;
        P.Num_PC_ChangeTimes = 1;
        P.Num_DCT_ChangeTimes = 1;
    }
    else
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of change times for levels of social distancing"       , "%i", (void*) & (P.Num_SD_ChangeTimes)    , 1, 1, 0)) P.Num_SD_ChangeTimes    = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of change times for levels of case isolation"          , "%i", (void*) & (P.Num_CI_ChangeTimes)    , 1, 1, 0)) P.Num_CI_ChangeTimes    = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of change times for levels of household quarantine"    , "%i", (void*) & (P.Num_HQ_ChangeTimes)    , 1, 1, 0)) P.Num_HQ_ChangeTimes    = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of change times for levels of place closure"           , "%i", (void*) & (P.Num_PC_ChangeTimes)    , 1, 1, 0)) P.Num_PC_ChangeTimes    = 1;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of change times for levels of digital contact tracing" , "%i", (void*) & (P.Num_DCT_ChangeTimes)   , 1, 1, 0)) P.Num_DCT_ChangeTimes   = 1;
    }

    P.SD_ChangeTimes    [0] = 0;
    P.CI_ChangeTimes    [0] = 0;
    P.HQ_ChangeTimes    [0] = 0;
    P.PC_ChangeTimes    [0] = 0;
    P.DCT_ChangeTimes   [0] = 0;
    for (int ChangeTime = 1; ChangeTime < MAX_NUM_INTERVENTION_CHANGE_TIMES; ChangeTime++)
    {
        P.SD_ChangeTimes    [ChangeTime] = 1e10;
        P.CI_ChangeTimes    [ChangeTime] = 1e10;
        P.HQ_ChangeTimes    [ChangeTime] = 1e10;
        P.PC_ChangeTimes    [ChangeTime] = 1e10;
        P.DCT_ChangeTimes   [ChangeTime] = 1e10;
    }
    GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Change times for levels of social distancing"      , "%lf", (void*)P.SD_ChangeTimes    , P.Num_SD_ChangeTimes  , 1, 0);
    GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Change times for levels of case isolation"         , "%lf", (void*)P.CI_ChangeTimes    , P.Num_CI_ChangeTimes  , 1, 0);
    GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Change times for levels of household quarantine"   , "%lf", (void*)P.HQ_ChangeTimes    , P.Num_HQ_ChangeTimes  , 1, 0);
    GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Change times for levels of place closure"          , "%lf", (void*)P.PC_ChangeTimes    , P.Num_PC_ChangeTimes  , 1, 0);
    GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Change times for levels of digital contact tracing", "%lf", (void*)P.DCT_ChangeTimes, P.Num_DCT_ChangeTimes    , 1, 0);
 
    // initialize to zero (regardless of whether doing places or households).
    for (int ChangeTime = 0; ChangeTime < MAX_NUM_INTERVENTION_CHANGE_TIMES; ChangeTime++)
    {
        P.SD_SpatialEffects_OverTime                [ChangeTime] = 0;
        P.Enhanced_SD_SpatialEffects_OverTime       [ChangeTime] = 0;
        P.CI_SpatialAndPlaceEffects_OverTime        [ChangeTime] = 0;
        P.HQ_SpatialEffects_OverTime                [ChangeTime] = 0;
        P.PC_SpatialEffects_OverTime                [ChangeTime] = 0;
        P.DCT_SpatialAndPlaceEffects_OverTime       [ChangeTime] = 0;

        P.SD_HouseholdEffects_OverTime          [ChangeTime] = 0;
        P.Enhanced_SD_HouseholdEffects_OverTime [ChangeTime] = 0;
        P.CI_HouseholdEffects_OverTime          [ChangeTime] = 0;
        P.HQ_HouseholdEffects_OverTime          [ChangeTime] = 0;
        P.PC_HouseholdEffects_OverTime          [ChangeTime] = 0;
        P.DCT_HouseholdEffects_OverTime         [ChangeTime] = 0;

        for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
        {
            P.SD_PlaceEffects_OverTime          [ChangeTime][PlaceType] = 0;
            P.Enhanced_SD_PlaceEffects_OverTime [ChangeTime][PlaceType] = 0;
            P.HQ_PlaceEffects_OverTime          [ChangeTime][PlaceType] = 0;
            P.PC_PlaceEffects_OverTime          [ChangeTime][PlaceType] = 0;
        }
        P.PC_Durs_OverTime[ChangeTime] = 0;

        P.CI_Prop_OverTime                  [ChangeTime] = 0;
        P.HQ_Individual_PropComply_OverTime [ChangeTime] = 0;
        P.HQ_Household_PropComply_OverTime  [ChangeTime] = 0;
        P.DCT_Prop_OverTime                 [ChangeTime] = 0;
    }
 

    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rates over time given social distancing"            , "%lf", (void*)P.SD_SpatialEffects_OverTime, P.Num_SD_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++) P.SD_SpatialEffects_OverTime[ChangeTime] = P.SocDistSpatialEffect; 
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rates over time given enhanced social distancing"   , "%lf", (void*)P.Enhanced_SD_SpatialEffects_OverTime, P.Num_SD_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++) P.Enhanced_SD_SpatialEffects_OverTime[ChangeTime] = P.EnhancedSocDistSpatialEffect; 
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual contacts after case isolation over time"                            , "%lf", (void*)P.CI_SpatialAndPlaceEffects_OverTime, P.Num_CI_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_CI_ChangeTimes; ChangeTime++) P.CI_SpatialAndPlaceEffects_OverTime[ChangeTime] = P.CaseIsolationEffectiveness;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual spatial contacts over time after household quarantine"              , "%lf", (void*)P.HQ_SpatialEffects_OverTime, P.Num_HQ_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_HQ_ChangeTimes; ChangeTime++) P.HQ_SpatialEffects_OverTime[ChangeTime] = P.HQuarantineSpatialEffect;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative spatial contact rates over time after place closure"                , "%lf", (void*)P.PC_SpatialEffects_OverTime, P.Num_PC_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) P.PC_SpatialEffects_OverTime[ChangeTime] = P.PlaceCloseSpatialRelContact;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual contacts after digital contact tracing isolation over time"         , "%lf", (void*)P.DCT_SpatialAndPlaceEffects_OverTime, P.Num_DCT_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_DCT_ChangeTimes; ChangeTime++) P.DCT_SpatialAndPlaceEffects_OverTime[ChangeTime] = P.DCTCaseIsolationEffectiveness;

    if (P.DoHouseholds)
    {
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rates over time given social distancing"          , "%lf", (void*)P.SD_HouseholdEffects_OverTime, P.Num_SD_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++) P.SD_HouseholdEffects_OverTime[ChangeTime] = P.SocDistHouseholdEffect;
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rates over time given enhanced social distancing" , "%lf", (void*)P.Enhanced_SD_HouseholdEffects_OverTime, P.Num_SD_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++) P.Enhanced_SD_HouseholdEffects_OverTime[ChangeTime] = P.EnhancedSocDistHouseholdEffect;
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual household contacts after case isolation over time"                  , "%lf", (void*)P.CI_HouseholdEffects_OverTime, P.Num_CI_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_CI_ChangeTimes; ChangeTime++) P.CI_HouseholdEffects_OverTime[ChangeTime] = P.CaseIsolationHouseEffectiveness;
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rates over time after quarantine"                 , "%lf", (void*)P.HQ_HouseholdEffects_OverTime, P.Num_HQ_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_HQ_ChangeTimes; ChangeTime++) P.HQ_HouseholdEffects_OverTime[ChangeTime] = P.HQuarantineHouseEffect;
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative household contact rates over time after place closure"              , "%lf", (void*)P.PC_HouseholdEffects_OverTime, P.Num_PC_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) P.PC_HouseholdEffects_OverTime[ChangeTime] = P.PlaceCloseHouseholdRelContact;
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual household contacts after digital contact tracing isolation over time", "%lf", (void*)P.DCT_HouseholdEffects_OverTime, P.Num_DCT_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_DCT_ChangeTimes; ChangeTime++) P.DCT_HouseholdEffects_OverTime[ChangeTime] = P.DCTCaseIsolationHouseEffectiveness;
    }

    if (P.DoPlaces)
    {
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative place contact rates over time given social distancing by place type", "%lf", (void*) &P.SD_PlaceEffects_OverTime[0][0], P.Num_SD_ChangeTimes * P.PlaceTypeNum, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++) 
                for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                    P.SD_PlaceEffects_OverTime[ChangeTime][PlaceType] = P.SocDistPlaceEffect[PlaceType];

        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Relative place contact rates over time given enhanced social distancing by place type", "%lf", (void*) &P.Enhanced_SD_PlaceEffects_OverTime[0][0], P.Num_SD_ChangeTimes * P.PlaceTypeNum, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++) 
                for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                    P.Enhanced_SD_PlaceEffects_OverTime[ChangeTime][PlaceType] = P.EnhancedSocDistPlaceEffect[PlaceType];

        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Residual place contacts over time after household quarantine by place type", "%lf", (void*) &P.HQ_PlaceEffects_OverTime[0][0], P.Num_HQ_ChangeTimes * P.PlaceTypeNum, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_HQ_ChangeTimes; ChangeTime++) 
                for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                    P.HQ_PlaceEffects_OverTime[ChangeTime][PlaceType] = P.HQuarantinePlaceEffect[PlaceType];

        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of places remaining open after closure by place type over time", "%lf", (void*) &P.PC_PlaceEffects_OverTime[0][0], P.Num_PC_ChangeTimes * P.PlaceTypeNum, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) 
                for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                    P.PC_PlaceEffects_OverTime[ChangeTime][PlaceType] = P.PlaceCloseEffect[PlaceType];
 
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportional attendance after closure by place type over time", "%lf", (void*) &P.PC_PropAttending_OverTime[0][0], P.Num_PC_ChangeTimes * P.PlaceTypeNum, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) 
                for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                    P.PC_PropAttending_OverTime[ChangeTime][PlaceType] = P.PlaceClosePropAttending[PlaceType];
    }
 

    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of detected cases isolated over time", "%lf", (void*)P.CI_Prop_OverTime, P.Num_CI_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_CI_ChangeTimes; ChangeTime++) P.CI_Prop_OverTime[ChangeTime] = P.CaseIsolationProp;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Individual level compliance with quarantine over time"   , "%lf", (void*)P.HQ_Individual_PropComply_OverTime, P.Num_HQ_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_HQ_ChangeTimes; ChangeTime++) P.HQ_Individual_PropComply_OverTime[ChangeTime] = P.HQuarantinePropIndivCompliant;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Household level compliance with quarantine over time"    , "%lf", (void*)P.HQ_Household_PropComply_OverTime, P.Num_HQ_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_HQ_ChangeTimes; ChangeTime++) P.HQ_Household_PropComply_OverTime[ChangeTime] = P.HQuarantinePropHouseCompliant;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of digital contacts who self-isolate over time", "%lf", (void*)P.DCT_Prop_OverTime, P.Num_DCT_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_DCT_ChangeTimes; ChangeTime++) P.DCT_Prop_OverTime[ChangeTime] = P.ProportionDigitalContactsIsolate;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Maximum number of contacts to trace per index case over time", "%i", (void*)P.DCT_MaxToTrace_OverTime, P.Num_DCT_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_DCT_ChangeTimes; ChangeTime++) P.DCT_MaxToTrace_OverTime[ChangeTime] = P.MaxDigitalContactsToTrace;
    if (P.DoPlaces)
    {
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure incidence threshold over time", "%lf", (void*)P.PC_IncThresh_OverTime, P.Num_PC_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) P.PC_IncThresh_OverTime[ChangeTime] = P.PlaceCloseIncTrig1;
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Place closure fractional incidence threshold over time", "%lf", (void*)P.PC_FracIncThresh_OverTime, P.Num_PC_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) P.PC_FracIncThresh_OverTime[ChangeTime] = P.PlaceCloseFracIncTrig;
        if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for place closure over time", "%i", (void*)P.PC_CellIncThresh_OverTime, P.Num_PC_ChangeTimes, 1, 0))
            for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) P.PC_CellIncThresh_OverTime[ChangeTime] = P.PlaceCloseCellIncThresh1;
        for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) if(P.PC_CellIncThresh_OverTime[ChangeTime]<0) P.PC_CellIncThresh_OverTime[ChangeTime] = 1000000000; // allows -1 to be used as a proxy for no cell-based triggering
    }
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Household quarantine trigger incidence per cell over time", "%lf", (void*)P.HQ_CellIncThresh_OverTime, P.Num_HQ_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_HQ_ChangeTimes; ChangeTime++) P.HQ_CellIncThresh_OverTime[ChangeTime] = P.HHQuar_CellIncThresh;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Case isolation trigger incidence per cell over time", "%lf", (void*)P.CI_CellIncThresh_OverTime, P.Num_CI_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_CI_ChangeTimes; ChangeTime++) P.CI_CellIncThresh_OverTime[ChangeTime] = P.CaseIsolation_CellIncThresh;
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for social distancing over time", "%i", (void*)P.SD_CellIncThresh_OverTime, P.Num_SD_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++) P.SD_CellIncThresh_OverTime[ChangeTime] = P.SocDistCellIncThresh;

    // place closure
    if (!P.VaryEfficaciesOverTime || !GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of place closure over time", "%lf", (void*)P.PC_Durs_OverTime, P.Num_PC_ChangeTimes, 1, 0))
        for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++) P.PC_Durs_OverTime[ChangeTime] = P.PlaceCloseDurationBase;

    if (P.VaryEfficaciesOverTime)
    {
        for (int SD_ChangeTime = P.Num_SD_ChangeTimes; SD_ChangeTime < MAX_NUM_INTERVENTION_CHANGE_TIMES - 1; SD_ChangeTime++)
        {
            P.SD_SpatialEffects_OverTime    [SD_ChangeTime] = P.SD_SpatialEffects_OverTime      [P.Num_SD_ChangeTimes - 1];
            P.SD_HouseholdEffects_OverTime  [SD_ChangeTime] = P.SD_HouseholdEffects_OverTime    [P.Num_SD_ChangeTimes - 1];
            for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                P.SD_PlaceEffects_OverTime[SD_ChangeTime][PlaceType] = P.SD_PlaceEffects_OverTime[P.Num_SD_ChangeTimes - 1][PlaceType];
            P.Enhanced_SD_SpatialEffects_OverTime   [SD_ChangeTime] = P.Enhanced_SD_SpatialEffects_OverTime     [P.Num_SD_ChangeTimes - 1];
            P.Enhanced_SD_HouseholdEffects_OverTime [SD_ChangeTime] = P.Enhanced_SD_HouseholdEffects_OverTime   [P.Num_SD_ChangeTimes - 1];
            for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                P.Enhanced_SD_PlaceEffects_OverTime[SD_ChangeTime][PlaceType] = P.Enhanced_SD_PlaceEffects_OverTime[P.Num_SD_ChangeTimes - 1][PlaceType];
 
            P.SD_CellIncThresh_OverTime             [SD_ChangeTime] = P.SD_CellIncThresh_OverTime               [P.Num_SD_ChangeTimes - 1];
        }

        for (int CI_ChangeTime = P.Num_CI_ChangeTimes; CI_ChangeTime < MAX_NUM_INTERVENTION_CHANGE_TIMES - 1; CI_ChangeTime++)
        {
            P.CI_SpatialAndPlaceEffects_OverTime[CI_ChangeTime] = P.CI_SpatialAndPlaceEffects_OverTime  [P.Num_CI_ChangeTimes - 1];
            P.CI_HouseholdEffects_OverTime      [CI_ChangeTime] = P.CI_HouseholdEffects_OverTime        [P.Num_CI_ChangeTimes - 1];
            P.CI_Prop_OverTime                  [CI_ChangeTime] = P.CI_Prop_OverTime                    [P.Num_CI_ChangeTimes - 1];
            P.CI_CellIncThresh_OverTime         [CI_ChangeTime] = P.CI_CellIncThresh_OverTime           [P.Num_CI_ChangeTimes - 1];
        }

        for (int HQ_ChangeTime = P.Num_HQ_ChangeTimes; HQ_ChangeTime < MAX_NUM_INTERVENTION_CHANGE_TIMES - 1; HQ_ChangeTime++)
        {
            P.HQ_SpatialEffects_OverTime    [HQ_ChangeTime] = P.HQ_SpatialEffects_OverTime  [P.Num_HQ_ChangeTimes - 1];
            P.HQ_HouseholdEffects_OverTime  [HQ_ChangeTime] = P.HQ_HouseholdEffects_OverTime[P.Num_HQ_ChangeTimes - 1];
            for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                P.HQ_PlaceEffects_OverTime[HQ_ChangeTime][PlaceType] = P.HQ_PlaceEffects_OverTime[P.Num_HQ_ChangeTimes - 1][PlaceType];
 
            P.HQ_Individual_PropComply_OverTime [HQ_ChangeTime] = P.HQ_Individual_PropComply_OverTime   [P.Num_HQ_ChangeTimes - 1];
            P.HQ_Household_PropComply_OverTime  [HQ_ChangeTime] = P.HQ_Household_PropComply_OverTime    [P.Num_HQ_ChangeTimes - 1];
 
            P.HQ_CellIncThresh_OverTime         [HQ_ChangeTime] = P.HQ_CellIncThresh_OverTime           [P.Num_HQ_ChangeTimes - 1];
        }

        for (int PC_ChangeTime = P.Num_PC_ChangeTimes; PC_ChangeTime < MAX_NUM_INTERVENTION_CHANGE_TIMES - 1; PC_ChangeTime++)
        {
            P.PC_SpatialEffects_OverTime    [PC_ChangeTime] = P.PC_SpatialEffects_OverTime  [P.Num_PC_ChangeTimes - 1];
            P.PC_HouseholdEffects_OverTime  [PC_ChangeTime] = P.PC_HouseholdEffects_OverTime[P.Num_PC_ChangeTimes - 1];
            for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
            {
                P.PC_PlaceEffects_OverTime[PC_ChangeTime][PlaceType] = P.PC_PlaceEffects_OverTime[P.Num_PC_ChangeTimes - 1][PlaceType];
                P.PC_PropAttending_OverTime[PC_ChangeTime][PlaceType] = P.PC_PropAttending_OverTime[P.Num_PC_ChangeTimes - 1][PlaceType];
            }
 
            P.PC_IncThresh_OverTime         [PC_ChangeTime] = P.PC_IncThresh_OverTime       [P.Num_PC_ChangeTimes - 1];
            P.PC_FracIncThresh_OverTime     [PC_ChangeTime] = P.PC_FracIncThresh_OverTime   [P.Num_PC_ChangeTimes - 1];
            P.PC_CellIncThresh_OverTime     [PC_ChangeTime] = P.PC_CellIncThresh_OverTime   [P.Num_PC_ChangeTimes - 1];
        }

        for (int DCT_ChangeTime = P.Num_DCT_ChangeTimes; DCT_ChangeTime < MAX_NUM_INTERVENTION_CHANGE_TIMES - 1; DCT_ChangeTime++)
        {
            P.DCT_SpatialAndPlaceEffects_OverTime   [DCT_ChangeTime] = P.DCT_SpatialAndPlaceEffects_OverTime[P.Num_DCT_ChangeTimes - 1];
            P.DCT_HouseholdEffects_OverTime         [DCT_ChangeTime] = P.DCT_HouseholdEffects_OverTime      [P.Num_DCT_ChangeTimes - 1];
            P.DCT_Prop_OverTime                     [DCT_ChangeTime] = P.DCT_Prop_OverTime                  [P.Num_DCT_ChangeTimes - 1];
            P.DCT_MaxToTrace_OverTime               [DCT_ChangeTime] = P.DCT_MaxToTrace_OverTime            [P.Num_DCT_ChangeTimes - 1];
        }
    }
 
    if (P.DoPlaces)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of key workers randomly distributed in the population", "%i", (void*) & (P.KeyWorkerPopNum), 1, 1, 0)) P.KeyWorkerPopNum = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Number of key workers in different places by place type", "%i", (void*)P.KeyWorkerPlaceNum, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.KeyWorkerPlaceNum[i] = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of staff who are key workers per chosen place by place type", "%lf", (void*)P.KeyWorkerPropInKeyPlaces, P.PlaceTypeNum, 1, 0))
            for (i = 0; i < NUM_PLACE_TYPES; i++) P.KeyWorkerPropInKeyPlaces[i] = 1.0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Trigger incidence per cell for key worker prophylaxis", "%i", (void*) & (P.KeyWorkerProphCellIncThresh), 1, 1, 0)) P.KeyWorkerProphCellIncThresh = 1000000000;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Key worker prophylaxis start time", "%lf", (void*) & (P.KeyWorkerProphTimeStartBase), 1, 1, 0)) P.KeyWorkerProphTimeStartBase = USHRT_MAX / P.TimeStepsPerDay;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Duration of key worker prophylaxis", "%lf", (void*) & (P.KeyWorkerProphDuration), 1, 1, 0)) P.KeyWorkerProphDuration = 0;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Time interval from start of key worker prophylaxis before policy restarted", "%lf", (void*) & (P.KeyWorkerProphRenewalDuration), 1, 1, 0)) P.KeyWorkerProphRenewalDuration = P.KeyWorkerProphDuration;
        if (P.DoHouseholds)
        {
            if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Proportion of key workers whose households are also treated as key workers", "%lf", (void*) & (P.KeyWorkerHouseProp), 1, 1, 0)) P.KeyWorkerHouseProp = 0;
        }
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Minimum radius for key worker prophylaxis", "%lf", (void*) & (P.KeyWorkerProphRadius), 1, 1, 0)) P.KeyWorkerProphRadius = 0;
    }
    else
    {
        P.KeyWorkerPopNum = 0;
        P.KeyWorkerProphTimeStartBase = 1e10;
    }
 
    //Added this to parameter list so that recording infection events (and the number to record) can easily be turned off and on: ggilani - 10/10/2014
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Record infection events", "%i", (void*) & (P.DoRecordInfEvents), 1, 1, 0)) P.DoRecordInfEvents = 0;
    if (P.DoRecordInfEvents)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max number of infection events to record", "%i", (void*) & (P.MaxInfEvents), 1, 1, 0)) P.MaxInfEvents = 1000;
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Record infection events per run", "%i", (void*) & (P.RecordInfEventsPerRun), 1, 1, 0)) P.RecordInfEventsPerRun = 0;
    }
    else
    {
        P.MaxInfEvents = 0;
    }
    //Include a limit to the number of infections to simulate, if this happens before time runs out
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Limit number of infections", "%i", (void*) & (P.LimitNumInfections), 1, 1, 0)) P.LimitNumInfections = 0;
    if (P.LimitNumInfections)
    {
        if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max number of infections", "%i", (void*) & (P.MaxNumInfections), 1, 1, 0)) P.MaxNumInfections = 60000;
    }
    //Add origin-destination matrix parameter
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Output origin destination matrix", "%i", (void*) & (P.DoOriginDestinationMatrix), 1, 1, 0)) P.DoOriginDestinationMatrix = 0;
 
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Mean child age gap", "%i", (void*) & (P.MeanChildAgeGap), 1, 1, 0)) P.MeanChildAgeGap=2;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Min adult age", "%i", (void*)&(P.MinAdultAge), 1, 1, 0)) P.MinAdultAge = 19;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max MF partner age gap", "%i", (void*) & (P.MaxMFPartnerAgeGap), 1, 1, 0)) P.MaxMFPartnerAgeGap = 5;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max FM partner age gap", "%i", (void*) & (P.MaxFMPartnerAgeGap), 1, 1, 0)) P.MaxFMPartnerAgeGap = 5;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Min parent age gap", "%i", (void*) & (P.MinParentAgeGap), 1, 1, 0)) P.MinParentAgeGap = 19;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max parent age gap", "%i", (void*) & (P.MaxParentAgeGap), 1, 1, 0)) P.MaxParentAgeGap = 44;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Max child age", "%i", (void*) & (P.MaxChildAge), 1, 1, 0)) P.MaxChildAge = 20;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "One Child Two Pers Prob", "%lf", (void*) & (P.OneChildTwoPersProb), 1, 1, 0)) P.OneChildTwoPersProb = 0.08;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Two Child Three Pers Prob", "%lf", (void*) & (P.TwoChildThreePersProb), 1, 1, 0)) P.TwoChildThreePersProb = 0.11;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "One Pers House Prob Old", "%lf", (void*) & (P.OnePersHouseProbOld), 1, 1, 0)) P.OnePersHouseProbOld = 0.5;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Two Pers House Prob Old", "%lf", (void*) & (P.TwoPersHouseProbOld), 1, 1, 0)) P.TwoPersHouseProbOld = 0.5;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "One Pers House Prob Young", "%lf", (void*) & (P.OnePersHouseProbYoung), 1, 1, 0)) P.OnePersHouseProbYoung = 0.23;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Two Pers House Prob Young", "%lf", (void*) & (P.TwoPersHouseProbYoung), 1, 1, 0)) P.TwoPersHouseProbYoung = 0.23;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "One Child Prob Youngest Child Under Five", "%lf", (void*) & (P.OneChildProbYoungestChildUnderFive), 1, 1, 0)) P.OneChildProbYoungestChildUnderFive = 0.5;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Two Children Prob Youngest Under Five", "%lf", (void*) & (P.TwoChildrenProbYoungestUnderFive), 1, 1, 0)) P.TwoChildrenProbYoungestUnderFive = 0.0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Prob Youngest Child Under Five", "%lf", (void*) & (P.ProbYoungestChildUnderFive), 1, 1, 0)) P.ProbYoungestChildUnderFive = 0;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Zero Child Three Pers Prob", "%lf", (void*) & (P.ZeroChildThreePersProb), 1, 1, 0)) P.ZeroChildThreePersProb = 0.25;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "One Child Four Pers Prob", "%lf", (void*) & (P.OneChildFourPersProb), 1, 1, 0)) P.OneChildFourPersProb = 0.2;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Young And Single Slope", "%lf", (void*) & (P.YoungAndSingleSlope), 1, 1, 0)) P.YoungAndSingleSlope = 0.7;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Young And Single", "%i", (void*) & (P.YoungAndSingle), 1, 1, 0)) P.YoungAndSingle = 36;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "No Child Pers Age", "%i", (void*) & (P.NoChildPersAge), 1, 1, 0)) P.NoChildPersAge = 44;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Old Pers Age", "%i", (void*) & (P.OldPersAge), 1, 1, 0)) P.OldPersAge = 60;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Three Child Five Pers Prob", "%lf", (void*) & (P.ThreeChildFivePersProb), 1, 1, 0)) P.ThreeChildFivePersProb = 0.5;
    if (!GetInputParameter2(ParamFile_dat, PreParamFile_dat, "Older Gen Gap", "%i", (void*) & (P.OlderGenGap), 1, 1, 0)) P.OlderGenGap = 19;
 
    // Close input files.
    fclose(ParamFile_dat);
    if (PreParamFile_dat != NULL) fclose(PreParamFile_dat);
    if (ParamFile_dat != AdminFile_dat && AdminFile_dat != NULL) fclose(AdminFile_dat);
 
    if (P.DoOneGen != 0) P.DoOneGen = 1;
    P.ColourPeriod = 2000;
    P.MoveRestrRadius2 = P.MoveRestrRadius * P.MoveRestrRadius;
    P.SocDistRadius2 = P.SocDistRadius * P.SocDistRadius;
    P.VaccRadius2 = P.VaccRadius * P.VaccRadius;
    P.VaccMinRadius2 = P.VaccMinRadius * P.VaccMinRadius;
    P.TreatRadius2 = P.TreatRadius * P.TreatRadius;
    P.PlaceCloseRadius2 = P.PlaceCloseRadius * P.PlaceCloseRadius;
    P.KeyWorkerProphRadius2 = P.KeyWorkerProphRadius * P.KeyWorkerProphRadius;
    if (P.TreatRadius2 == 0) P.TreatRadius2 = -1;
    if (P.VaccRadius2 == 0) P.VaccRadius2 = -1;
    if (P.PlaceCloseRadius2 == 0) P.PlaceCloseRadius2 = -1;
    if (P.MoveRestrRadius2 == 0) P.MoveRestrRadius2 = -1;
    if (P.SocDistRadius2 == 0) P.SocDistRadius2 = -1;
    if (P.KeyWorkerProphRadius2 == 0) P.KeyWorkerProphRadius2 = -1;
/*  if (P.TreatCellIncThresh < 1) P.TreatCellIncThresh = 1;
    if (P.CaseIsolation_CellIncThresh < 1) P.CaseIsolation_CellIncThresh = 1;
    if (P.DigitalContactTracing_CellIncThresh < 1) P.DigitalContactTracing_CellIncThresh = 1;
    if (P.HHQuar_CellIncThresh < 1) P.HHQuar_CellIncThresh = 1;
    if (P.MoveRestrCellIncThresh < 1) P.MoveRestrCellIncThresh = 1;
    if (P.PlaceCloseCellIncThresh < 1) P.PlaceCloseCellIncThresh = 1;
    if (P.KeyWorkerProphCellIncThresh < 1) P.KeyWorkerProphCellIncThresh = 1;
*/

    P.usHQuarantineHouseDuration = ((unsigned short int) (P.HQuarantineHouseDuration * P.TimeStepsPerDay));
    P.usVaccTimeToEfficacy = ((unsigned short int) (P.VaccTimeToEfficacy * P.TimeStepsPerDay));
    P.usVaccTimeEfficacySwitch = ((unsigned short int) (P.VaccTimeEfficacySwitch * P.TimeStepsPerDay));
    P.usCaseIsolationDelay = ((unsigned short int) (P.CaseIsolationDelay * P.TimeStepsPerDay));
    P.usCaseIsolationDuration = ((unsigned short int) (P.CaseIsolationDuration * P.TimeStepsPerDay));
    P.usCaseAbsenteeismDuration = ((unsigned short int) (P.CaseAbsenteeismDuration * P.TimeStepsPerDay));
    P.usCaseAbsenteeismDelay = ((unsigned short int) (P.CaseAbsenteeismDelay * P.TimeStepsPerDay));
    if (P.DoUTM_coords)
    {
        for (i = 0; i <= 1000; i++)
        {
            asin2sqx[i] = asin(sqrt(((double)(i)) / 1000));
            asin2sqx[i] = asin2sqx[i] * asin2sqx[i];
        }
        for (t = 0; t <= 360; t++)
        {
            sinx[(int)t] = sin(PI * t / 180);
            cosx[(int)t] = cos(PI * t / 180);
        }
    }
    fprintf(stderr, "Parameters read\n");
}
void ReadInterventions(char* IntFile)
{
    FILE* dat;
    double r, s, startt, stopt;
    int j, k, au, ni, f, nsr;
    char buf[65536], txt[65536];
    Intervention CurInterv;
 
    fprintf(stderr, "Reading intervention file.\n");
    if (!(dat = fopen(IntFile, "rb"))) ERR_CRITICAL("Unable to open intervention file\n");
    if(fscanf(dat, "%*[^<]") != 0) { // needs to be separate line because start of file
        ERR_CRITICAL("fscanf failed in ReadInterventions\n");
    }
    if(fscanf(dat, "<%[^>]", txt) != 1) {
        ERR_CRITICAL("fscanf failed in ReadInterventions\n");
    }
    if (strcmp(txt, "\?xml version=\"1.0\" encoding=\"ISO-8859-1\"\?") != 0) ERR_CRITICAL("Intervention file not XML.\n");
    if(fscanf(dat, "%*[^<]<%[^>]", txt) != 1) {
        ERR_CRITICAL("fscanf failed in ReadInterventions\n");
    }
    if (strcmp(txt, "InterventionSettings") != 0) ERR_CRITICAL("Intervention has no top level.\n");
    ni = 0;
    while (!feof(dat))
    {
        if(fscanf(dat, "%*[^<]<%[^>]", txt) != 1) {
            ERR_CRITICAL("fscanf failed in ReadInterventions\n");
        }
        if (strcmp(txt, "intervention") == 0)
        {
            ni++;
            if(fscanf(dat, "%*[^<]<%[^>]", txt) != 1) {
                ERR_CRITICAL("fscanf failed in ReadInterventions\n");
            }
            if (strcmp(txt, "parameters") != 0) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            if (!GetXMLNode(dat, "Type", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            if (strcmp(txt, "Treatment") == 0)
                CurInterv.InterventionType = 0;
            else if (strcmp(txt, "Vaccination") == 0)
                CurInterv.InterventionType = 1;
            else if (strcmp(txt, "ITN") == 0)
                CurInterv.InterventionType = 2;
            else if (strcmp(txt, "IRS") == 0)
                CurInterv.InterventionType = 3;
            else if (strcmp(txt, "GM") == 0)
                CurInterv.InterventionType = 4;
            else if (strcmp(txt, "MSAT") == 0)
                CurInterv.InterventionType = 5;
            else
                sscanf(txt, "%i", &CurInterv.InterventionType);
            if (!GetXMLNode(dat, "AUThresh", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%i", &CurInterv.DoAUThresh);
            if (!GetXMLNode(dat, "StartTime", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.StartTime);
            startt = CurInterv.StartTime;
            if (!GetXMLNode(dat, "StopTime", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.StopTime);
            stopt = CurInterv.StopTime;
            if (!GetXMLNode(dat, "MinDuration", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.MinDuration);
            CurInterv.MinDuration *= DAYS_PER_YEAR;
            if (!GetXMLNode(dat, "RepeatInterval", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.RepeatInterval);
            CurInterv.RepeatInterval *= DAYS_PER_YEAR;
            if (!GetXMLNode(dat, "MaxPrevAtStart", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.StartThresholdHigh);
            if (!GetXMLNode(dat, "MinPrevAtStart", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.StartThresholdLow);
            if (!GetXMLNode(dat, "MaxPrevAtStop", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.StopThreshold);
            if (GetXMLNode(dat, "NoStartAfterMinDur", "parameters", txt, 1))
                sscanf(txt, "%i", &CurInterv.NoStartAfterMin);
            else
                CurInterv.NoStartAfterMin = 0;
            if (!GetXMLNode(dat, "Level", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%lf", &CurInterv.Level);
            if (GetXMLNode(dat, "LevelCellVar", "parameters", txt, 1))
                sscanf(txt, "%lf", &CurInterv.LevelCellVar);
            else
                CurInterv.LevelCellVar = 0;
            if (GetXMLNode(dat, "LevelAUVar", "parameters", txt, 1))
                sscanf(txt, "%lf", &CurInterv.LevelAUVar);
            else
                CurInterv.LevelCellVar = 0;
            if (GetXMLNode(dat, "LevelCountryVar", "parameters", txt, 1))
                sscanf(txt, "%lf", &CurInterv.LevelCountryVar);
            else
                CurInterv.LevelCellVar = 0;
            if (GetXMLNode(dat, "LevelClustering", "parameters", txt, 1))
                sscanf(txt, "%lf", &CurInterv.LevelClustering);
            else
                CurInterv.LevelClustering = 0;
            if (GetXMLNode(dat, "ControlParam", "parameters", txt, 1))
                sscanf(txt, "%lf", &CurInterv.ControlParam);
            else
                CurInterv.ControlParam = 0;
            if (GetXMLNode(dat, "TimeOffset", "parameters", txt, 1))
                sscanf(txt, "%lf", &CurInterv.TimeOffset);
            else
                CurInterv.TimeOffset = 0;
 
            if (!GetXMLNode(dat, "MaxRounds", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%u", &CurInterv.MaxRounds);
            if (!GetXMLNode(dat, "MaxResource", "parameters", txt, 1)) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            sscanf(txt, "%u", &CurInterv.MaxResource);
            if (GetXMLNode(dat, "NumSequentialReplicas", "parameters", txt, 1))
                sscanf(txt, "%i", &nsr);
            else
                nsr = 0;
            do {
                if(fscanf(dat, "%*[^<]<%[^>]", txt) != 1) {
                    ERR_CRITICAL("fscanf failed in ReadInterventions\n");
                }
            } while ((strcmp(txt, "/intervention") != 0) && (strcmp(txt, "/parameters") != 0) && (!feof(dat)));
            if (strcmp(txt, "/parameters") != 0) ERR_CRITICAL("Incomplete intervention parameter specification in intervention file\n");
            if(fscanf(dat, "%*[^<]<%[^>]", txt) != 1) {
                ERR_CRITICAL("fscanf failed in ReadInterventions\n");
            }
            if ((strcmp(txt, "adunits") != 0) && (strcmp(txt, "countries") != 0)) ERR_CRITICAL("Incomplete adunits/countries specification in intervention file\n");
            if (strcmp(txt, "adunits") == 0)
            {
                while (GetXMLNode(dat, "A", "adunits", buf, 0))
                {
                    sscanf(buf, "%s", txt);
                    j = atoi(txt);
                    if (j == 0)
                    {
                        f = 1; au = -1;
                        do
                        {
                            au++; f = strcmp(txt, AdUnits[au].ad_name);
                        } while ((f) && (au < P.NumAdunits));
                        if (!f)
                        {
                            r = fabs(CurInterv.Level) + (2.0 * ranf() - 1) * CurInterv.LevelAUVar;
                            if ((CurInterv.Level < 1) && (r > 1))
                                r = 1;
                            else if (r < 0)
                                r = 0;
                            for (k = 0; k <= nsr; k++)
                            {
                                AdUnits[au].InterventionList[AdUnits[au].NI] = CurInterv;
                                AdUnits[au].InterventionList[AdUnits[au].NI].Level = r;
                                AdUnits[au].InterventionList[AdUnits[au].NI].StartTime = startt + ((double)k) * (stopt - startt);
                                AdUnits[au].InterventionList[AdUnits[au].NI].StopTime = stopt + ((double)k) * (stopt - startt);
                                AdUnits[au].NI++;
                            }
                        }
                    }
                    else
                    {
                        k = (j % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor;
                        au = P.AdunitLevel1Lookup[k];
                        if ((au >= 0) && (AdUnits[au].id / P.AdunitLevel1Divisor == j / P.AdunitLevel1Divisor))
                        {
                            r = CurInterv.Level + (2.0 * ranf() - 1) * CurInterv.LevelAUVar;
                            if ((CurInterv.Level < 1) && (r > 1))
                                r = 1;
                            else if (r < 0)
                                r = 0;
                            for (k = 0; k <= nsr; k++)
                            {
                                AdUnits[au].InterventionList[AdUnits[au].NI] = CurInterv;
                                AdUnits[au].InterventionList[AdUnits[au].NI].Level = r;
                                AdUnits[au].InterventionList[AdUnits[au].NI].StartTime = startt + ((double)k) * (stopt - startt);
                                AdUnits[au].InterventionList[AdUnits[au].NI].StopTime = stopt + ((double)k) * (stopt - startt);
                                AdUnits[au].NI++;
                            }
                        }
                    }
                }
            }
            else
            {
                while (GetXMLNode(dat, "C", "countries", buf, 0))
                {
                    s = (2.0 * ranf() - 1) * CurInterv.LevelCountryVar;
                    sscanf(buf, "%s", txt);
                    j = atoi(txt);
                    for (au = 0; au < P.NumAdunits; au++)
                        if (((j == 0) && (strcmp(txt, AdUnits[au].cnt_name) == 0)) || ((j > 0) && (j == AdUnits[au].cnt_id)))
                        {
                            r = CurInterv.Level + (2.0 * ranf() - 1) * CurInterv.LevelAUVar + s;
                            if ((CurInterv.Level < 1) && (r > 1))
                                r = 1;
                            else if (r < 0)
                                r = 0;
                            for (k = 0; k <= nsr; k++)
                            {
                                AdUnits[au].InterventionList[AdUnits[au].NI] = CurInterv;
                                AdUnits[au].InterventionList[AdUnits[au].NI].Level = r;
                                AdUnits[au].InterventionList[AdUnits[au].NI].StartTime = startt + ((double)k) * (stopt - startt);
                                AdUnits[au].InterventionList[AdUnits[au].NI].StopTime = stopt + ((double)k) * (stopt - startt);
                                AdUnits[au].NI++;
                            }
                        }
                }
            }
            if(fscanf(dat, "%*[^<]<%[^>]", txt) != 1) {
                ERR_CRITICAL("fscanf failed in ReadInterventions\n");
            }
            if (strcmp(txt, "/intervention") != 0) ERR_CRITICAL("Incorrect intervention specification in intervention file\n");
        }
    }
    if (strcmp(txt, "/InterventionSettings") != 0) ERR_CRITICAL("Intervention has no top level closure.\n");
    fprintf(stderr, "%i interventions read\n", ni);
    fclose(dat);
}
int GetXMLNode(FILE* dat, const char* NodeName, const char* ParentName, char* Value, int ResetFilePos)
{
    // ResetFilePos=1 leaves dat cursor in same position as when function was called. 0 leaves it at end of NodeName closure
    // GetXMLNode returns 1 if NodeName found, 0 otherwise. If NodeName not found, ParentName closure must be
 
    char buf[65536], CloseNode[2048], CloseParent[2048];
    int CurPos, ret;
 
    sprintf(CloseParent, "/%s", ParentName);
    CurPos = ftell(dat);
    do
    {
        if(fscanf(dat, "%*[^<]<%[^>]", buf) != 1) {
            ERR_CRITICAL("fscanf failed in GetXMLNode");
        }
    } while ((strcmp(buf, CloseParent) != 0) && (strcmp(buf, NodeName) != 0) && (!feof(dat)));
    if (strcmp(buf, CloseParent) == 0)
        ret = 0;
    else
    {
        if (strcmp(buf, NodeName) != 0) ERR_CRITICAL("Incomplete node specification in XML file\n");
        if(fscanf(dat, ">%[^<]", buf) != 1) {
            ERR_CRITICAL("fscanf failed in GetXMLNode");
        }
        if (strlen(buf) < 2048) strcpy(Value, buf);
        //      fprintf(stderr,"# %s=%s\n",NodeName,Value);
        if(fscanf(dat, "<%[^>]", buf) != 1) {
            ERR_CRITICAL("fscanf failed in GetXMLNode");
        }
        sprintf(CloseNode, "/%s", NodeName);
        if (strcmp(buf, CloseNode) != 0) ERR_CRITICAL("Incomplete node specification in XML file\n");
        ret = 1;
    }
    if (ResetFilePos) fseek(dat, CurPos, 0);
    return ret;
}
void ReadAirTravel(char* AirTravelFile)
{
    int i, j, k, l;
    float sc, t, t2;
    float* buf;
    double traf;
    char outname[1024];
    FILE* dat;
 
    fprintf(stderr, "Reading airport data...\nAirports with no connections = ");
    if (!(dat = fopen(AirTravelFile, "rb"))) ERR_CRITICAL("Unable to open airport file\n");
    if(fscanf(dat, "%i %i", &P.Nairports, &P.Air_popscale) != 2) {
        ERR_CRITICAL("fscanf failed in void ReadAirTravel\n");
    }
    sc = (float)((double)P.PopSize / (double)P.Air_popscale);
    if (P.Nairports > MAX_AIRPORTS) ERR_CRITICAL("Too many airports\n");
    if (P.Nairports < 2) ERR_CRITICAL("Too few airports\n");
    if (!(buf = (float*)calloc(P.Nairports + 1, sizeof(float)))) ERR_CRITICAL("Unable to allocate airport storage\n");
    if (!(Airports = (Airport*)calloc(P.Nairports, sizeof(Airport)))) ERR_CRITICAL("Unable to allocate airport storage\n");
    for (i = 0; i < P.Nairports; i++)
    {
        if(fscanf(dat, "%f %f %lf", &(Airports[i].loc_x), &(Airports[i].loc_y), &traf) != 3) {
            ERR_CRITICAL("fscanf failed in void ReadAirTravel\n");
        }
        traf *= (P.AirportTrafficScale * sc);
        if ((Airports[i].loc_x < P.SpatialBoundingBox[0]) || (Airports[i].loc_x >= P.SpatialBoundingBox[2])
            || (Airports[i].loc_y < P.SpatialBoundingBox[1]) || (Airports[i].loc_y >= P.SpatialBoundingBox[3]))
        {
            Airports[i].loc_x = Airports[i].loc_y = -1;
            Airports[i].total_traffic = 0;
        }
        else
        {
            //fprintf(stderr,"(%f\t%f) ",Airports[i].loc_x,Airports[i].loc_y);
            Airports[i].loc_x -= (float)P.SpatialBoundingBox[0];
            Airports[i].loc_y -= (float)P.SpatialBoundingBox[1];
            Airports[i].total_traffic = (float)traf;
        }
        t = 0;
        for (j = k = 0; j < P.Nairports; j++)
        {
            if(fscanf(dat, "%f", buf + j) != 1) {
                ERR_CRITICAL("fscanf failed in void ReadAirTravel\n");
            }
            if (buf[j] > 0) { k++; t += buf[j]; }
        }
        Airports[i].num_connected = k;
        if (Airports[i].num_connected > 0)
        {
            if (!(Airports[i].prop_traffic = (float*)calloc(Airports[i].num_connected, sizeof(float)))) ERR_CRITICAL("Unable to allocate airport storage\n");
            if (!(Airports[i].conn_airports = (unsigned short int*) calloc(Airports[i].num_connected, sizeof(unsigned short int)))) ERR_CRITICAL("Unable to allocate airport storage\n");
            for (j = k = 0; j < P.Nairports; j++)
                if (buf[j] > 0)
                {
                    Airports[i].conn_airports[k] = j;
                    Airports[i].prop_traffic[k] = buf[j] / t;
                    k++;
                }
        }
        else
        {
            if (Airports[i].total_traffic > 0)
                fprintf(stderr, "#%i# ", i);
            else
                fprintf(stderr, "%i ", i);
        }
    }
    fclose(dat);
    free(buf);
    fprintf(stderr, "\nAirport data read OK.\n");
    for (i = 0; i < P.Nairports; i++)
    {
        /*      fprintf(stderr,"(%f %i|",Airports[i].total_traffic,Airports[i].num_connected);
        */      t = 0; k = 0;
    for (j = Airports[i].num_connected - 1; j >= 0; j--)
    {
        if ((Airports[i].prop_traffic[j] > 0) && (Airports[Airports[i].conn_airports[j]].total_traffic == 0))
        {
            t += Airports[i].prop_traffic[j];
            Airports[i].num_connected--;
            if (j < Airports[i].num_connected)
            {
                Airports[i].prop_traffic[j] = Airports[i].prop_traffic[Airports[i].num_connected];
                Airports[i].conn_airports[j] = Airports[i].conn_airports[Airports[i].num_connected];
            }
            Airports[i].prop_traffic[Airports[i].num_connected] = 0;
            Airports[i].conn_airports[Airports[i].num_connected] = 0;
        }
        else if (Airports[i].prop_traffic[j] > 0)
            k = 1;
    }
    /*      fprintf(stderr,"%f %i ",t,k);
    */      t = 1.0f - t;
    if (k)
    {
        Airports[i].total_traffic *= t;
        t2 = 0;
        for (j = 0; j < Airports[i].num_connected; j++)
        {
            Airports[i].prop_traffic[j] = t2 + Airports[i].prop_traffic[j];
            t2 = Airports[i].prop_traffic[j];
        }
        for (j = 0; j < Airports[i].num_connected; j++)
            Airports[i].prop_traffic[j] /= t2;
        /*          if((Airports[i].num_connected>0)&&(Airports[i].prop_traffic[Airports[i].num_connected-1]!=1))
                        fprintf(stderr,"<%f> ",Airports[i].prop_traffic[Airports[i].num_connected-1]);
        */
    }
    else
    {
        Airports[i].total_traffic = 0; Airports[i].num_connected = 0;
    }
    if (Airports[i].num_connected > 0)
    {
        for (j = k = 0; k < 128; k++)
        {
            t = (float)((double)k / 128);
            while (Airports[i].prop_traffic[j] < t) j++;
            Airports[i].Inv_prop_traffic[k] = j;
        }
        Airports[i].Inv_prop_traffic[128] = Airports[i].num_connected - 1;
    }
    /*      fprintf(stderr,"%f) ",Airports[i].total_traffic);
    */
    }
    fprintf(stderr, "Airport data clipped OK.\n");
    for (i = 0; i < MAX_DIST; i++) AirTravelDist[i] = 0;
    for (i = 0; i < P.Nairports; i++)
        if (Airports[i].total_traffic > 0)
        {
            for (j = 0; j < Airports[i].num_connected; j++)
            {
                k = (int)Airports[i].conn_airports[j];
                traf = floor(sqrt(dist2_raw(Airports[i].loc_x, Airports[i].loc_y, Airports[k].loc_x, Airports[k].loc_y)) / OUTPUT_DIST_SCALE);
                l = (int)traf;
                //fprintf(stderr,"%(%i) ",l);
                if (l < MAX_DIST)
                    AirTravelDist[l] += Airports[i].total_traffic * Airports[i].prop_traffic[j];
            }
        }
    sprintf(outname, "%s.airdist.xls", OutFile);
    if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open air travel output file\n");
    fprintf(dat, "dist\tfreq\n");
    for (i = 0; i < MAX_DIST; i++)
        fprintf(dat, "%i\t%.10f\n", i, AirTravelDist[i]);
    fclose(dat);
}
 
void InitModel(int run) // passing run number so we can save run number in the infection event log: ggilani - 15/10/2014
{
    int nim;
    int nsi[MAX_NUM_SEED_LOCATIONS];
 
    if (P.OutputBitmap)
    {
#ifdef _WIN32
        //if (P.OutputBitmap == 1)
        //{
        //  char buf[200];
        //  sprintf(buf, "%s.ge" DIRECTORY_SEPARATOR "%s.avi", OutFile, OutFile);
        //  avi = CreateAvi(buf, P.BitmapMovieFrame, NULL);
        //}
#endif
        for (unsigned p = 0; p < bmh->imagesize; p++)
        {
            bmInfected[p] = bmRecovered[p] = bmTreated[p] = 0;
        }
    }
    ns = 0;
    State.S = P.PopSize;
    State.L = State.I = State.R = State.D = 0;
    State.cumI = State.cumR = State.cumC = State.cumFC = State.cumH = State.cumCT = State.cumCC = State.cumTC = State.cumD = State.cumDC = State.trigDC = State.DCT = State.cumDCT
        = State.cumHQ
        = State.cumAC = State.cumAH = State.cumAA = State.cumACS
        = State.cumAPC = State.cumAPA = State.cumAPCS = 0;
    State.cumT = State.cumUT = State.cumTP = State.cumV = State.sumRad2 = State.maxRad2 = State.cumV_daily = State.cumVG = 0; //added State.cumVG
    State.mvacc_cum = 0;
    if (P.DoSeverity)
    {
        State.Mild      = State.ILI         = State.SARI    = State.Critical    = State.CritRecov       = 0;
        State.cumMild   = State.cumILI      = State.cumSARI = State.cumCritical = State.cumCritRecov    = 0;
        State.cumDeath_ILI = State.cumDeath_SARI = State.cumDeath_Critical = 0;
 
        for (int AdminUnit = 0; AdminUnit <= P.NumAdunits; AdminUnit++)
        {
            State.Mild_adunit[AdminUnit] = State.ILI_adunit[AdminUnit] =
            State.SARI_adunit[AdminUnit] = State.Critical_adunit[AdminUnit] = State.CritRecov_adunit[AdminUnit] =
            State.cumMild_adunit[AdminUnit] = State.cumILI_adunit[AdminUnit] =
            State.cumSARI_adunit[AdminUnit] = State.cumCritical_adunit[AdminUnit] = State.cumCritRecov_adunit[AdminUnit] =
            State.cumDeath_ILI_adunit[AdminUnit] = State.cumDeath_SARI_adunit[AdminUnit] = State.cumDeath_Critical_adunit[AdminUnit] =
            State.cumD_adunit[AdminUnit] = 0;
        }
        for (int AgeGroup = 0; AgeGroup < NUM_AGE_GROUPS; AgeGroup++)
        {
            State.Mild_age[AgeGroup] = State.ILI_age[AgeGroup] =
                State.SARI_age[AgeGroup] = State.Critical_age[AgeGroup] = State.CritRecov_age[AgeGroup] =
                State.cumMild_age[AgeGroup] = State.cumILI_age[AgeGroup] =
                State.cumSARI_age[AgeGroup] = State.cumCritical_age[AgeGroup] = State.cumCritRecov_age[AgeGroup] =
                State.cumDeath_ILI_age[AgeGroup] = State.cumDeath_SARI_age[AgeGroup] = State.cumDeath_Critical_age[AgeGroup] = 0;
        }
    }
 
    for (int i = 0; i < NUM_AGE_GROUPS; i++) State.cumCa[i] = State.cumIa[i] = State.cumDa[i] = 0;
    for (int i = 0; i < 2; i++) State.cumC_keyworker[i] = State.cumI_keyworker[i] = State.cumT_keyworker[i] = 0;
    for (int i = 0; i < NUM_PLACE_TYPES; i++) State.NumPlacesClosed[i] = 0;
    for (int i = 0; i < INFECT_TYPE_MASK; i++) State.cumItype[i] = 0;
    //initialise cumulative case counts per country to zero: ggilani 12/11/14
    for (int i = 0; i < MAX_COUNTRIES; i++) State.cumC_country[i] = 0;
    if (P.DoAdUnits)
        for (int i = 0; i <= P.NumAdunits; i++)
        {
            State.cumI_adunit[i] = State.cumC_adunit[i] = State.cumD_adunit[i] = State.cumT_adunit[i] = State.cumH_adunit[i] =
                State.cumDC_adunit[i] = State.cumCT_adunit[i] = State.cumCC_adunit[i] = State.trigDC_adunit[i] = State.DCT_adunit[i] = State.cumDCT_adunit[i] = 0; //added hospitalisation, added detected cases, contact tracing per adunit, cases who are contacts: ggilani 03/02/15, 15/06/17
            AdUnits[i].place_close_trig = 0;
            AdUnits[i].CaseIsolationTimeStart = AdUnits[i].HQuarantineTimeStart = AdUnits[i].DigitalContactTracingTimeStart = AdUnits[i].SocialDistanceTimeStart = AdUnits[i].PlaceCloseTimeStart = 1e10;
            AdUnits[i].ndct = 0; //noone being digitally contact traced at beginning of run
        }
 
    //update state variables for storing contact distribution
    for (int i = 0; i < MAX_CONTACTS+1; i++) State.contact_dist[i] = 0;
 
    for (int j = 0; j < MAX_NUM_THREADS; j++)
    {
        StateT[j].L = StateT[j].I = StateT[j].R = StateT[j].D = 0;
        StateT[j].cumI = StateT[j].cumR = StateT[j].cumC = StateT[j].cumFC = StateT[j].cumH = StateT[j].cumCT = StateT[j].cumCC = StateT[j].DCT = StateT[j].cumDCT = StateT[j].cumTC = StateT[j].cumD = StateT[j].cumDC
            = StateT[j].cumHQ = StateT[j].cumAC = StateT[j].cumACS
            = StateT[j].cumAH = StateT[j].cumAA = StateT[j].cumAPC = StateT[j].cumAPA = StateT[j].cumAPCS = 0;
        StateT[j].cumT = StateT[j].cumUT = StateT[j].cumTP = StateT[j].cumV = StateT[j].sumRad2 = StateT[j].maxRad2 = StateT[j].cumV_daily =  0;
        for (int i = 0; i < NUM_AGE_GROUPS; i++) StateT[j].cumCa[i] = StateT[j].cumIa[i] = StateT[j].cumDa[i] = 0;
        for (int i = 0; i < 2; i++) StateT[j].cumC_keyworker[i] = StateT[j].cumI_keyworker[i] = StateT[j].cumT_keyworker[i] = 0;
        for (int i = 0; i < NUM_PLACE_TYPES; i++) StateT[j].NumPlacesClosed[i] = 0;
        for (int i = 0; i < INFECT_TYPE_MASK; i++) StateT[j].cumItype[i] = 0;
        //initialise cumulative case counts per country per thread to zero: ggilani 12/11/14
        for (int i = 0; i < MAX_COUNTRIES; i++) StateT[j].cumC_country[i] = 0;
        if (P.DoAdUnits)
            for (int i = 0; i <= P.NumAdunits; i++)
                StateT[j].cumI_adunit[i] = StateT[j].cumC_adunit[i] = StateT[j].cumD_adunit[i] = StateT[j].cumT_adunit[i] = StateT[j].cumH_adunit[i] = StateT[j].cumDC_adunit[i] =
                StateT[j].cumCT_adunit[i] = StateT[j].cumCC_adunit[i] = StateT[j].nct_queue[i] = StateT[j].cumDCT_adunit[i] = StateT[j].DCT_adunit[i] = StateT[j].ndct_queue[i] = 0; //added hospitalisation, detected cases, contact tracing per adunit, cases who are contacts: ggilani 03/02/15, 15/06/17
 
        if (P.DoSeverity)
        {
            StateT[j].Mild      = StateT[j].ILI     = StateT[j].SARI    = StateT[j].Critical    = StateT[j].CritRecov       = 0;
            StateT[j].cumMild   = StateT[j].cumILI  = StateT[j].cumSARI = StateT[j].cumCritical = StateT[j].cumCritRecov    = 0;
            StateT[j].cumDeath_ILI = StateT[j].cumDeath_SARI = StateT[j].cumDeath_Critical = 0;
 
            for (int AdminUnit = 0; AdminUnit <= P.NumAdunits; AdminUnit++)
            {
                StateT[j].Mild_adunit[AdminUnit] = StateT[j].ILI_adunit[AdminUnit] =
                StateT[j].SARI_adunit[AdminUnit] = StateT[j].Critical_adunit[AdminUnit] = StateT[j].CritRecov_adunit[AdminUnit] =
                StateT[j].cumMild_adunit[AdminUnit] = StateT[j].cumILI_adunit[AdminUnit] =
                StateT[j].cumSARI_adunit[AdminUnit] = StateT[j].cumCritical_adunit[AdminUnit] = StateT[j].cumCritRecov_adunit[AdminUnit] =
                StateT[j].cumDeath_ILI_adunit[AdminUnit] = StateT[j].cumDeath_SARI_adunit[AdminUnit] = StateT[j].cumDeath_Critical_adunit[AdminUnit] =
                StateT[j].cumD_adunit[AdminUnit] =  0;
            }
            for (int AgeGroup = 0; AgeGroup < NUM_AGE_GROUPS; AgeGroup++)
            {
                StateT[j].Mild_age[AgeGroup] = StateT[j].ILI_age[AgeGroup] =
                    StateT[j].SARI_age[AgeGroup] = StateT[j].Critical_age[AgeGroup] = StateT[j].CritRecov_age[AgeGroup] =
                    StateT[j].cumMild_age[AgeGroup] = StateT[j].cumILI_age[AgeGroup] =
                    StateT[j].cumSARI_age[AgeGroup] = StateT[j].cumCritical_age[AgeGroup] = StateT[j].cumCritRecov_age[AgeGroup] =
                    StateT[j].cumDeath_ILI_age[AgeGroup] = StateT[j].cumDeath_SARI_age[AgeGroup] = StateT[j].cumDeath_Critical_age[AgeGroup] = 0;
            }
 
        }
        //resetting thread specific parameters for storing contact distribution
        for (int i = 0; i < MAX_CONTACTS+1; i++) StateT[j].contact_dist[i] = 0;
 
    }
    nim = 0;
 
#pragma omp parallel for schedule(static,1) default(none) \
        shared(P, Hosts)
    for (int tn = 0; tn < P.NumThreads; tn++)
        for (int k = tn; k < P.PopSize; k+= P.NumThreads)
        {
            Hosts[k].absent_start_time = USHRT_MAX - 1;
            Hosts[k].absent_stop_time = 0;
            if (P.DoAirports) Hosts[k].PlaceLinks[P.HotelPlaceType] = -1;
            Hosts[k].vacc_start_time = Hosts[k].treat_start_time = Hosts[k].quar_start_time = Hosts[k].isolation_start_time = Hosts[k].absent_start_time = Hosts[k].dct_start_time = Hosts[k].dct_trigger_time = USHRT_MAX - 1;
            Hosts[k].treat_stop_time = Hosts[k].absent_stop_time = Hosts[k].dct_end_time = 0;
            Hosts[k].quar_comply = 2;
            Hosts[k].to_die = 0;
            Hosts[k].Travelling = 0;
            Hosts[k].detected = 0; //set detected to zero initially: ggilani - 19/02/15
            Hosts[k].detected_time = 0;
            Hosts[k].digitalContactTraced = 0;
            Hosts[k].inf = InfStat_Susceptible;
            Hosts[k].num_treats = 0;
            Hosts[k].latent_time = Hosts[k].recovery_or_death_time = 0; //also set hospitalisation time to zero: ggilani 28/10/2014
            Hosts[k].infector = -1;
            Hosts[k].infect_type = 0;
            Hosts[k].index_case_dct = 0;
            Hosts[k].ProbAbsent =(float) ranf_mt(tn);
            Hosts[k].ProbCare = (float) ranf_mt(tn);
            Hosts[k].susc = (float)((P.DoPartialImmunity) ? (1.0 - P.InitialImmunity[HOST_AGE_GROUP(k)]) : 1.0);
            if(P.SusceptibilitySD > 0) Hosts[k].susc *= (float) gen_gamma_mt(1 / (P.SusceptibilitySD * P.SusceptibilitySD), 1 / (P.SusceptibilitySD * P.SusceptibilitySD), tn);
            if (P.DoSeverity)
            {
                Hosts[k].SARI_time = USHRT_MAX - 1; 
                Hosts[k].Critical_time = USHRT_MAX - 1;
                Hosts[k].RecoveringFromCritical_time = USHRT_MAX - 1;
                Hosts[k].Severity_Current = Severity_Asymptomatic;
                Hosts[k].Severity_Final = Severity_Asymptomatic;
                Hosts[k].inf = InfStat_Susceptible;
            }
        }
 
#pragma omp parallel for reduction(+:nim) schedule(static,1) default(none) \
        shared(P, Cells, Hosts, Households)
    for (int tn = 0; tn < P.NumThreads; tn++)
    {
        for (int i = tn; i < P.NC; i+=P.NumThreads)
        {
            if ((Cells[i].tot_treat != 0) || (Cells[i].tot_vacc != 0) || (Cells[i].S != Cells[i].n) || (Cells[i].D > 0) || (Cells[i].R > 0))
            {
                for (int j = 0; j < Cells[i].n; j++)
                {
                    int k = Cells[i].members[j];
                    Cells[i].susceptible[j] = k; //added this in here instead
                    Hosts[k].listpos = j;
                }
                Cells[i].S = Cells[i].n;
                Cells[i].L = Cells[i].I = Cells[i].R = Cells[i].cumTC = Cells[i].D = 0;
                Cells[i].infected = Cells[i].latent = Cells[i].susceptible + Cells[i].S;
                Cells[i].tot_treat = Cells[i].tot_vacc = 0;
                for (int l = 0; l < MAX_INTERVENTION_TYPES; l++) Cells[i].CurInterv[l] = -1;
 
                // Next loop needs to count down for DoImmune host list reordering to work
                if(!P.DoPartialImmunity)
                    for (int j = Cells[i].n - 1; j >= 0; j--)
                    {
                        int k = Cells[i].members[j];
                        if (P.DoWholeHouseholdImmunity)
                        {
    // note that this breaks determinism of runs if executed due to reordering of Cell members list each realisation
                            if (P.InitialImmunity[0] != 0)
                            {
                                if (Households[Hosts[k].hh].FirstPerson == k)
                                {
                                    if ((P.InitialImmunity[0] == 1) || (ranf_mt(tn) < P.InitialImmunity[0]))
                                    {
                                        nim += Households[Hosts[k].hh].nh;
                                        for (int m = Households[Hosts[k].hh].nh - 1; m >= 0; m--)
                                            DoImmune(k + m);
                                    }
                                }
                            }
                        }
                        else
                        {
                            int m = HOST_AGE_GROUP(k);
                            if ((P.InitialImmunity[m] == 1) || ((P.InitialImmunity[m] > 0) && (ranf_mt(tn) < P.InitialImmunity[m])))
                            {
                                DoImmune(k); nim += 1;
                            }
                        }
                    }
            }
        }
    }
 
#pragma omp parallel for schedule(static,500) default(none) \
        shared(P, Mcells, McellLookup)
    for (int l = 0; l < P.NMCP; l++)
    {
        int i = (int)(McellLookup[l] - Mcells);
        Mcells[i].vacc_start_time = Mcells[i].treat_start_time = USHRT_MAX - 1;
        Mcells[i].treat_end_time = 0;
        Mcells[i].treat_trig = Mcells[i].vacc_trig = Mcells[i].vacc = Mcells[i].treat = 0;
        Mcells[i].place_trig = Mcells[i].move_trig = Mcells[i].socdist_trig = Mcells[i].keyworkerproph_trig =
            Mcells[i].placeclose = Mcells[i].moverest = Mcells[i].socdist = Mcells[i].keyworkerproph = 0;
        Mcells[i].move_start_time = USHRT_MAX - 1;
        Mcells[i].place_end_time = Mcells[i].move_end_time =
            Mcells[i].socdist_end_time = Mcells[i].keyworkerproph_end_time = 0;
    }
    if (P.DoPlaces)
#pragma omp parallel for schedule(static,1) default(none) \
            shared(P, Places)
        for (int m = 0; m < P.PlaceTypeNum; m++)
        {
            for(int l = 0; l < P.Nplace[m]; l++)
            {
                Places[m][l].close_start_time = USHRT_MAX - 1;
                Places[m][l].treat = Places[m][l].control_trig = 0;
                Places[m][l].treat_end_time = Places[m][l].close_end_time = 0;
                Places[m][l].ProbClose = (float) ranf_mt(m);
                if (P.AbsenteeismPlaceClosure)
                {
                    Places[m][l].AbsentLastUpdateTime = 0;
                    for (int i2 = 0; i2 < P.MaxAbsentTime; i2++) Places[m][l].Absent[i2] = 0;
                }
            }
        }

    P.SocDistDurationCurrent            = P.SocDistDuration;
    P.SocDistSpatialEffectCurrent       = P.SD_SpatialEffects_OverTime  [0];                
    P.SocDistHouseholdEffectCurrent     = P.SD_HouseholdEffects_OverTime[0];                
    for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
        P.SocDistPlaceEffectCurrent[PlaceType] = P.SD_PlaceEffects_OverTime[0][PlaceType];  
    P.SocDistCellIncThresh              = P.SD_CellIncThresh_OverTime   [0];                

    P.EnhancedSocDistSpatialEffectCurrent       = P.Enhanced_SD_SpatialEffects_OverTime     [0];    
    P.EnhancedSocDistHouseholdEffectCurrent     = P.Enhanced_SD_HouseholdEffects_OverTime   [0];    
    for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
        P.EnhancedSocDistPlaceEffectCurrent[PlaceType] = P.Enhanced_SD_PlaceEffects_OverTime[0][PlaceType]; 

    P.CaseIsolationEffectiveness        = P.CI_SpatialAndPlaceEffects_OverTime  [0];    
    P.CaseIsolationHouseEffectiveness   = P.CI_HouseholdEffects_OverTime        [0];    
    P.CaseIsolationProp                 = P.CI_Prop_OverTime                    [0];    
    P.CaseIsolation_CellIncThresh       = P.CI_CellIncThresh_OverTime           [0];    
 

    P.HQuarantineSpatialEffect  = P.HQ_SpatialEffects_OverTime  [0];    
    P.HQuarantineHouseEffect    = P.HQ_HouseholdEffects_OverTime[0];    
    for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
        P.HQuarantinePlaceEffect[PlaceType] = P.HQ_PlaceEffects_OverTime    [0][PlaceType]; 
    P.HQuarantinePropIndivCompliant = P.HQ_Individual_PropComply_OverTime   [0]; 
    P.HQuarantinePropHouseCompliant = P.HQ_Household_PropComply_OverTime    [0]; 
    P.HHQuar_CellIncThresh          = P.HQ_CellIncThresh_OverTime           [0]; 
 

    P.PlaceCloseSpatialRelContact   = P.PC_SpatialEffects_OverTime  [0];            
    P.PlaceCloseHouseholdRelContact = P.PC_HouseholdEffects_OverTime[0];            
    for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
    {
        P.PlaceCloseEffect[PlaceType] = P.PC_PlaceEffects_OverTime[0][PlaceType];   
        P.PlaceClosePropAttending[PlaceType] = P.PC_PropAttending_OverTime[0][PlaceType];
    }
    P.PlaceCloseIncTrig1            = P.PC_IncThresh_OverTime       [0];            
    P.PlaceCloseFracIncTrig         = P.PC_FracIncThresh_OverTime   [0];            
    P.PlaceCloseCellIncThresh1      = P.PC_CellIncThresh_OverTime   [0];            
    P.PlaceCloseDurationBase = P.PC_Durs_OverTime[0]; 
 

    P.DCTCaseIsolationEffectiveness         = P.DCT_SpatialAndPlaceEffects_OverTime [0];    
    P.DCTCaseIsolationHouseEffectiveness    = P.DCT_HouseholdEffects_OverTime       [0];    
    P.ProportionDigitalContactsIsolate      = P.DCT_Prop_OverTime                   [0];    
    P.MaxDigitalContactsToTrace             = P.DCT_MaxToTrace_OverTime             [0];
 
 
 
    for (int i = 0; i < MAX_NUM_THREADS; i++)
    {
        for (int j = 0; j < MAX_NUM_THREADS; j++)   StateT[i].n_queue[j] = 0;
        for (int j = 0; j < P.PlaceTypeNum; j++)    StateT[i].np_queue[j] = 0;
    }
    if (DoInitUpdateProbs)
    {
        UpdateProbs(0);
        DoInitUpdateProbs = 0;
    }
    //initialise event log to zero at the beginning of every run: ggilani - 10/10/2014. UPDATE: 15/10/14 - we are now going to store all events from all realisations in one file
    if ((P.DoRecordInfEvents) && (P.RecordInfEventsPerRun))
    {
        nEvents = 0;
        for (int i = 0; i < P.MaxInfEvents; i++)
        {
            InfEventLog[i].t = InfEventLog[i].infectee_x = InfEventLog[i].infectee_y = InfEventLog[i].t_infector = 0.0;
            InfEventLog[i].infectee_ind = InfEventLog[i].infector_ind = 0;
            InfEventLog[i].infectee_adunit = InfEventLog[i].listpos = InfEventLog[i].infectee_cell = InfEventLog[i].infector_cell = InfEventLog[i].thread = 0;
        }
    }
 
    for (int i = 0; i < P.NumSeedLocations; i++) nsi[i] = (int) (((double) P.NumInitialInfections[i]) * P.InitialInfectionsAdminUnitWeight[i]* P.SeedingScaling +0.5);
    SeedInfection(0, nsi, 0, run);
    P.ControlPropCasesId = P.PreAlertControlPropCasesId;
    P.TreatTimeStart = 1e10;
 
    P.VaccTimeStart = 1e10;
    P.MoveRestrTimeStart = 1e10;
    P.PlaceCloseTimeStart = 1e10;
    P.PlaceCloseTimeStart2 = 2e10;
    P.SocDistTimeStart = 1e10;
    P.AirportCloseTimeStart = 1e10;
    //P.DigitalContactTracingTimeStart = 1e10;
    P.HQuarantineTimeStart = 1e10;
    P.KeyWorkerProphTimeStart = 1e10;
    P.TreatMaxCourses = P.TreatMaxCoursesBase;
    P.VaccMaxCourses = P.VaccMaxCoursesBase;
    P.PlaceCloseDuration = P.PlaceCloseDurationBase; 
    P.PlaceCloseIncTrig = P.PlaceCloseIncTrig1;
    P.PlaceCloseTimeStartPrevious = 1e10;
    P.PlaceCloseCellIncThresh = P.PlaceCloseCellIncThresh1;
    P.ResetSeedsFlag = 0; //added this to allow resetting seeds part way through run: ggilani 27/11/2019
    if (!P.StopCalibration) P.PreControlClusterIdTime = 0;
 
    fprintf(stderr, "Finished InitModel.\n");
}
 
void SeedInfection(double t, int* nsi, int rf, int run) //adding run number to pass it to event log
{
    /* *nsi is an array of the number of seeding infections by location. During runtime, usually just a single int (given by a poisson distribution)*/
    /*rf set to 0 when initializing model, otherwise set to 1 during runtime. */
 
    int i /*seed location index*/;
    int j /*microcell number*/;
    int k, l /*k,l are grid coords at first, then l changed to be person within Microcell j, then k changed to be index of new infection*/;
    int m = 0/*guard against too many infections and infinite loop*/;
    int f /*range = {0, 1000}*/;
    int n /*number of seed locations?*/;
 
    n = ((rf == 0) ? P.NumSeedLocations : 1);
    for (i = 0; i < n; i++)
    {
        if ((!P.DoRandomInitialInfectionLoc) || ((P.DoAllInitialInfectioninSameLoc) && (rf))) 
        {
            k = (int)(P.LocationInitialInfection[i][0] / P.in_microcells_.width_);
            l = (int)(P.LocationInitialInfection[i][1] / P.in_microcells_.height_);
            j = k * P.get_number_of_micro_cells_high() + l;
            m = 0;
            for (k = 0; (k < nsi[i]) && (m < 10000); k++)
            {
                l = Mcells[j].members[(int)(ranf() * ((double)Mcells[j].n))]; 
                if (Hosts[l].inf == InfStat_Susceptible) 
                {
                    if (CalcPersonSusc(l, 0, 0, 0) > 0)
                    {
                        //only reset the initial location if rf==0, i.e. when initial seeds are being set, not when imported cases are being set
                        if (rf == 0)
                        {
                            P.LocationInitialInfection[i][0] = Households[Hosts[l].hh].loc_x;
                            P.LocationInitialInfection[i][1] = Households[Hosts[l].hh].loc_y;
                        }
                        Hosts[l].infector = -2;
                        Hosts[l].infect_type = INFECT_TYPE_MASK - 1;
                        DoInfect(l, t, 0, run); 
                        m = 0;
                    }
                }
                else { k--; m++; } 
            }
        }
        else if (P.DoAllInitialInfectioninSameLoc)
        {
            f = 0;
            do
            {
                m = 0;
                do
                {
                    l = (int)(ranf() * ((double)P.PopSize));
                    j = Hosts[l].mcell;
                    //fprintf(stderr,"%i ",AdUnits[Mcells[j].adunit].id);
                } while ((Mcells[j].n < nsi[i]) || (Mcells[j].n > P.MaxPopDensForInitialInfection)
                    || (Mcells[j].n < P.MinPopDensForInitialInfection)
                    || ((P.InitialInfectionsAdminUnit[i] > 0) && ((AdUnits[Mcells[j].adunit].id % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor != (P.InitialInfectionsAdminUnit[i] % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor)));
                for (k = 0; (k < nsi[i]) && (m < 10000); k++)
                {
                    l = Mcells[j].members[(int)(ranf() * ((double)Mcells[j].n))];
                    if (Hosts[l].inf == InfStat_Susceptible)
                    {
                        if (CalcPersonSusc(l, 0, 0, 0) > 0)
                        {
                            P.LocationInitialInfection[i][0] = Households[Hosts[l].hh].loc_x;
                            P.LocationInitialInfection[i][1] = Households[Hosts[l].hh].loc_y;
                            Hosts[l].infector = -2; Hosts[l].infect_type = INFECT_TYPE_MASK - 1;
                            DoInfect(l, t, 0, run);
                            m = 0;
                        }
                    }
                    else
                    {
                        k--; m++;
                    }
                }
                if (m)
                    f++;
                else
                    f = 0;
            } while ((f > 0) && (f < 1000));
        }
        else
        {
            m = 0;
            for (k = 0; (k < nsi[i]) && (m < 10000); k++)
            {
                do
                {
                    l = (int)(ranf() * ((double)P.PopSize));
                    j = Hosts[l].mcell;
                    //fprintf(stderr,"@@ %i %i ",AdUnits[Mcells[j].adunit].id, (int)(AdUnits[Mcells[j].adunit].id / P.CountryDivisor));
                } while ((Mcells[j].n == 0) || (Mcells[j].n > P.MaxPopDensForInitialInfection)
                    || (Mcells[j].n < P.MinPopDensForInitialInfection)
                    || ((P.InitialInfectionsAdminUnit[i] > 0) && ((AdUnits[Mcells[j].adunit].id % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor != (P.InitialInfectionsAdminUnit[i] % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor)));
                l = Mcells[j].members[(int)(ranf() * ((double)Mcells[j].n))];
                if (Hosts[l].inf == InfStat_Susceptible)
                {
                    if (CalcPersonSusc(l, 0, 0, 0) > 0)
                    {
                        P.LocationInitialInfection[i][0] = Households[Hosts[l].hh].loc_x;
                        P.LocationInitialInfection[i][1] = Households[Hosts[l].hh].loc_y;
                        Hosts[l].infector = -2; Hosts[l].infect_type = INFECT_TYPE_MASK - 1;
                        DoInfect(l, t, 0, run);
                        m = 0;
                    }
                    else
                    {
                        k--; m++;
                    }
                }
                else
                {
                    k--; m++;
                }
            }
        }
    }
    if (m > 0) fprintf(stderr, "### Seeding error ###\n");
}
 
 
int RunModel(int run) //added run number as parameter
{
    int j, k, l, fs, fs2, nu, ni, nsi[MAX_NUM_SEED_LOCATIONS] /*Denotes either Num imported Infections given rate ir, or number false positive "infections"*/;
    double ir; // infection import rate?;
    double t, cI, lcI, t2;
    unsigned short int ts;
    int continueEvents = 1;
 
 
/*  fprintf(stderr, "Checking consistency of initial state...\n");
    int i, i2, k2;
    for (i = j = k = ni = fs2 = i2 = 0; i < P.N; i++)
    {
        if (i % 1000 == 0) fprintf(stderr, "\r*** %i              ", i);
        if (Hosts[i].inf == 0) j++;
        if ((Hosts[i].pcell < P.NC) && (Hosts[i].pcell >= 0))
        {
            if (Cells[Hosts[i].pcell].susceptible[Hosts[i].listpos] != i)
            {
                k++;
                for (l = fs = 0; (l < Cells[Hosts[i].pcell].n) && (!fs); l++)
                    fs = (Cells[Hosts[i].pcell].susceptible[l] == i);
                if (!fs) ni++;
            }
            else
            {
                if ((Hosts[i].listpos > Cells[Hosts[i].pcell].S - 1) && (Hosts[i].inf == InfStat_Susceptible)) i2++;
                if ((Hosts[i].listpos < Cells[Hosts[i].pcell].S + Cells[Hosts[i].pcell].L + Cells[Hosts[i].pcell].I - 1) && (abs(Hosts[i].inf) == InfStat_Recovered)) i2++;
            }
            if ((Cells[Hosts[i].pcell].S + Cells[Hosts[i].pcell].L + Cells[Hosts[i].pcell].I + Cells[Hosts[i].pcell].R + Cells[Hosts[i].pcell].D) != Cells[Hosts[i].pcell].n)
            {
                k2++;
            }
        }
        else
            fs2++;
    }
    fprintf(stderr, "\n*** susceptibles=%i\nincorrect listpos=%i\nhosts not found in cell list=%i\nincorrect cell refs=%i\nincorrect positioning in cell susc list=%i\nwrong cell totals=%i\n", j, k, ni, fs2, i2, k2);
*/
    InterruptRun = 0;
    lcI = 1;
    if (P.DoLoadSnapshot)
    {
        P.ts_age = (int)(P.SnapshotLoadTime * P.TimeStepsPerDay);
        t = ((double)P.ts_age) * P.TimeStep;
    }
    else
    {
        t = 0;
        P.ts_age = 0;
    }
    fs = 1;
    fs2 = 0;
    nu = 0;
 
    for (ns = 1; ((ns < P.NumSamples) && (!InterruptRun)); ns++) //&&(continueEvents) <-removed this
    {
        RecordSample(t, ns - 1);
        fprintf(stderr, "\r    t=%lg   %i    %i|%i    %i     %i [=%i]  %i (%lg %lg %lg)   %lg    ", t,
            State.S, State.L, State.I, State.R, State.D, State.S + State.L + State.I + State.R + State.D, State.cumD, State.cumT, State.cumV, State.cumVG, sqrt(State.maxRad2) / 1000); //added State.cumVG
        if (!InterruptRun)
        {
            //Only run to a certain number of infections: ggilani 28/10/14
            if (P.LimitNumInfections) continueEvents = (State.cumI < P.MaxNumInfections);
 
            for (j = 0; ((j < P.UpdatesPerSample) && (!InterruptRun) && (continueEvents)); j++)
            {
                ts = (unsigned short int) (P.TimeStepsPerDay * t);
 
                //if we are to reset random numbers after an intervention event, specific time
                if (P.ResetSeedsPostIntervention)
                    if ((P.ResetSeedsFlag == 0) && (ts >= (P.TimeToResetSeeds * P.TimeStepsPerDay)))
                    {
                        setall(&P.nextRunSeed1, &P.nextRunSeed2);
                        P.ResetSeedsFlag = 1;
                    }
 
                if (fs)
                {
                    if (P.DoAirports) TravelDepartSweep(t);
                    k = (int)t;
                    if (P.DurImportTimeProfile > 0)
                    {
                        if (k < P.DurImportTimeProfile)
                            ir = P.ImportInfectionTimeProfile[k] * ((t > P.InfectionImportChangeTime) ? (P.InfectionImportRate2 / P.InfectionImportRate1) : 1.0);
                        else
                            ir = 0;
                    }
                    else    ir = (t > P.InfectionImportChangeTime) ? P.InfectionImportRate2 : P.InfectionImportRate1;
                    if (ir > 0) 
                    {
                        for (k = ni = 0; k < P.NumSeedLocations; k++) ni += (nsi[k] = (int)ignpoi(P.TimeStep * ir * P.InitialInfectionsAdminUnitWeight[k] * P.SeedingScaling)); 
                        if (ni > 0)     SeedInfection(t, nsi, 1, run);
                    }
                    if (P.FalsePositivePerCapitaIncidence > 0)
                    {
                        ni = (int)ignpoi(P.TimeStep * P.FalsePositivePerCapitaIncidence * ((double)P.PopSize));
                        if (ni > 0)
                        {
                            for (k = 0; k < ni; k++)
                            {
                                do
                                {
                                    l = (int)(((double)P.PopSize) * ranf()); 
                                } while ((abs(Hosts[l].inf) == InfStat_Dead) || (ranf() > P.FalsePositiveAgeRate[HOST_AGE_GROUP(l)]));
                                DoFalseCase(l, t, ts, 0);
                            }
                        }
                    }
                    InfectSweep(t, run);  // loops over all infectious people and decides which susceptible people to infect (at household, place and spatial level), and adds them to queue. Then changes each person's various characteristics using DoInfect function.  adding run number as a parameter to infect sweep so we can track run number: ggilani - 15/10/14
                    if (!P.DoSI) IncubRecoverySweep(t, run);
                    // If doing new contact tracing, update numbers of people under contact tracing after each time step
 
                    if (P.DoDigitalContactTracing) DigitalContactTracingSweep(t);
 
                    nu++;
                    fs2 = ((P.DoDeath) || (State.L + State.I > 0) || (ir > 0) || (P.FalsePositivePerCapitaIncidence > 0));
                    if (!TreatSweep(t))
                    {
                        if ((!fs2) && (State.L + State.I == 0) && (P.FalsePositivePerCapitaIncidence == 0)) { if ((ir == 0) && (((int)t) > P.DurImportTimeProfile)) fs = 0; }
                    }
                    if (P.DoAirports) TravelReturnSweep(t);
                }
                t += P.TimeStep;
                if (P.DoDeath) P.ts_age++;
                if ((P.DoSaveSnapshot) && (t <= P.SnapshotSaveTime) && (t + P.TimeStep > P.SnapshotSaveTime)) SaveSnapshot();
                if (t > P.TreatNewCoursesStartTime) P.TreatMaxCourses += P.TimeStep * P.TreatNewCoursesRate;
                if ((t > P.VaccNewCoursesStartTime) && (t < P.VaccNewCoursesEndTime)) P.VaccMaxCourses += P.TimeStep * P.VaccNewCoursesRate;
                cI = ((double)(State.S)) / ((double)P.PopSize);
                if ((lcI - cI) > 0.2)
                {
                    lcI = cI;
                    UpdateProbs(0);
                    DoInitUpdateProbs = 1;
                }
            }
        }
    }
    if (!InterruptRun) RecordSample(t, P.NumSamples - 1);
    fprintf(stderr, "\nEnd of run\n");
    t2 = t + P.SampleTime;
//  if(!InterruptRun)
    while (fs)
    {
        fs = TreatSweep(t2);
        t2 += P.SampleStep;
    }
    //  fprintf(stderr,"End RunModel\n");
    if (P.DoAirports)
    {
        t2 = t;
        for (t2 = t; t2 <= t + MAX_TRAVEL_TIME; t2 += P.TimeStep)
            TravelReturnSweep(t2);
    }
/*  if (!InterruptRun)
    {
        fprintf(stderr, "Checking consistency of final state...\n");
        int i, i2, k2;
        for (i = j = k = ni = fs2 = i2 = 0; i < P.PopSize; i++)
        {
            if (i % 1000 == 0) fprintf(stderr, "\r*** %i              ", i);
            if (Hosts[i].inf == 0) j++;
            if ((Hosts[i].pcell < P.NC) && (Hosts[i].pcell >= 0))
            {
                if (Cells[Hosts[i].pcell].susceptible[Hosts[i].listpos] != i)
                {
                    k++;
                    for (l = fs = 0; (l < Cells[Hosts[i].pcell].n) && (!fs); l++)
                        fs = (Cells[Hosts[i].pcell].susceptible[l] == i);
                    if (!fs) ni++;
                }
                else
                {
                    if ((Hosts[i].listpos > Cells[Hosts[i].pcell].S - 1) && (Hosts[i].inf == InfStat_Susceptible)) i2++;
                    if ((Hosts[i].listpos < Cells[Hosts[i].pcell].S + Cells[Hosts[i].pcell].L + Cells[Hosts[i].pcell].I - 1) && (abs(Hosts[i].inf) == InfStat_Recovered)) i2++;
                }
                if ((Cells[Hosts[i].pcell].S + Cells[Hosts[i].pcell].L + Cells[Hosts[i].pcell].I + Cells[Hosts[i].pcell].R + Cells[Hosts[i].pcell].D) != Cells[Hosts[i].pcell].n)
                {
                    k2++;
                }
            }
            else
                fs2++;
        }
        fprintf(stderr, "\n*** susceptibles=%i\nincorrect listpos=%i\nhosts not found in cell list=%i\nincorrect cell refs=%i\nincorrect positioning in cell susc list=%i\nwrong cell totals=%i\n", j, k, ni, fs2, i2, k2);
    }
*/
    if(!InterruptRun) RecordInfTypes();
    return (InterruptRun);
}
 
void SaveDistribs(void)
{
    int i, j, k;
    FILE* dat;
    char outname[1024];
    double s;
 
    if (P.DoPlaces)
    {
        for (j = 0; j < P.PlaceTypeNum; j++)
            if (j != P.HotelPlaceType)
            {
                for (i = 0; i < P.Nplace[j]; i++)
                    Places[j][i].n = 0;
                for (i = 0; i < P.PopSize; i++)
                {
                    if (Hosts[i].PlaceLinks[j] >= P.Nplace[j])
                        fprintf(stderr, "*%i %i: %i %i", i, j, Hosts[i].PlaceLinks[j], P.Nplace[j]);
                    else if (Hosts[i].PlaceLinks[j] >= 0)
                        Places[j][Hosts[i].PlaceLinks[j]].n++;
                }
            }
        for (j = 0; j < P.PlaceTypeNum; j++)
            for (i = 0; i < MAX_DIST; i++)
                PlaceDistDistrib[j][i] = 0;
        for (i = 0; i < P.PopSize; i++)
            for (j = 0; j < P.PlaceTypeNum; j++)
                if ((j != P.HotelPlaceType) && (Hosts[i].PlaceLinks[j] >= 0))
                {
                    if (Hosts[i].PlaceLinks[j] >= P.Nplace[j])
                        fprintf(stderr, "*%i %i: %i ", i, j, Hosts[i].PlaceLinks[j]);
                    else if ((!P.DoOutputPlaceDistForOneAdunit) ||
                        ((AdUnits[Mcells[Hosts[i].mcell].adunit].id % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor == (P.OutputPlaceDistAdunit % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor))
                    {
                        k = Hosts[i].PlaceLinks[j];
                        s = sqrt(dist2_raw(Households[Hosts[i].hh].loc_x, Households[Hosts[i].hh].loc_y, Places[j][k].loc_x, Places[j][k].loc_y)) / OUTPUT_DIST_SCALE;
                        k = (int)s;
                        if (k < MAX_DIST) PlaceDistDistrib[j][k]++;
                    }
                }
        for (j = 0; j < P.PlaceTypeNum; j++)
            for (i = 0; i < MAX_PLACE_SIZE; i++)
                PlaceSizeDistrib[j][i] = 0;
        for (j = 0; j < P.PlaceTypeNum; j++)
            if (j != P.HotelPlaceType)
                for (i = 0; i < P.Nplace[j]; i++)
                    if (Places[j][i].n < MAX_PLACE_SIZE)
                        PlaceSizeDistrib[j][Places[j][i].n]++;
        sprintf(outname, "%s.placedist.xls", OutFile);
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "dist");
        for (j = 0; j < P.PlaceTypeNum; j++)
            if (j != P.HotelPlaceType)
                fprintf(dat, "\tfreq_p%i", j);
        fprintf(dat, "\n");
        for (i = 0; i < MAX_DIST; i++)
        {
            fprintf(dat, "%i", i);
            for (j = 0; j < P.PlaceTypeNum; j++)
                if (j != P.HotelPlaceType)
                    fprintf(dat, "\t%i", PlaceDistDistrib[j][i]);
            fprintf(dat, "\n");
        }
        fclose(dat);
        sprintf(outname, "%s.placesize.xls", OutFile);
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "size");
        for (j = 0; j < P.PlaceTypeNum; j++)
            if (j != P.HotelPlaceType)
                fprintf(dat, "\tfreq_p%i", j);
        fprintf(dat, "\n");
        for (i = 0; i < MAX_PLACE_SIZE; i++)
        {
            fprintf(dat, "%i", i);
            for (j = 0; j < P.PlaceTypeNum; j++)
                if (j != P.HotelPlaceType)
                    fprintf(dat, "\t%i", PlaceSizeDistrib[j][i]);
            fprintf(dat, "\n");
        }
        fclose(dat);
    }
}
void SaveOriginDestMatrix(void)
{
    int i, j;
    FILE* dat;
    char outname[1024];
 
    sprintf(outname, "%s.origdestmat.xls", OutFile);
    if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
    fprintf(dat, "0,");
    for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "%i,", (AdUnits[i].id % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor);
    fprintf(dat, "\n");
    for (i = 0; i < P.NumAdunits; i++)
    {
        fprintf(dat, "%i,", (AdUnits[i].id % P.AdunitLevel1Mask) / P.AdunitLevel1Divisor);
        for (j = 0; j < P.NumAdunits; j++)
        {
            fprintf(dat, "%.10f,", AdUnits[i].origin_dest[j]);
        }
        fprintf(dat, "\n");
    }
    fclose(dat);
}
 
void SaveResults(void)
{
    int i, j;
    FILE* dat;
    char outname[1024];
 
    if (P.OutputNonSeverity)
    {
        sprintf(outname, "%s.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t\tS\tL\tI\tR\tD\tincI\tincR\tincFC\tincC\tincDC\tincTC\tincH\tincCT\tincCC\tcumT\tcumTP\tcumV\tcumVG\tExtinct\trmsRad\tmaxRad\n");//\t\t%.10f\t%.10f\t%.10f\n",P.R0household,P.R0places,P.R0spatial);
        for(i = 0; i < P.NumSamples; i++)
        {
            fprintf(dat, "%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\n",
                TimeSeries[i].t, TimeSeries[i].S, TimeSeries[i].L, TimeSeries[i].I,
                TimeSeries[i].R, TimeSeries[i].D, TimeSeries[i].incI,
                TimeSeries[i].incR, TimeSeries[i].incFC, TimeSeries[i].incC, TimeSeries[i].incDC, TimeSeries[i].incTC, TimeSeries[i].incH, TimeSeries[i].incCT, TimeSeries[i].incCC,
                TimeSeries[i].cumT, TimeSeries[i].cumTP, TimeSeries[i].cumV, TimeSeries[i].cumVG, TimeSeries[i].extinct, TimeSeries[i].rmsRad, TimeSeries[i].maxRad);
        }
        fclose(dat);
    }
 
    if ((P.DoAdUnits) && (P.DoAdunitOutput))
    {
        sprintf(outname, "%s.adunit.xls", OutFile);
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t");
        for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tI_%s", AdUnits[i].ad_name);
        for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tC_%s", AdUnits[i].ad_name);
        for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tDC_%s", AdUnits[i].ad_name);
 
        fprintf(dat, "\n");
        for (i = 0; i < P.NumSamples; i++)
        {
            fprintf(dat, "%.10f", TimeSeries[i].t);
            for (j = 0; j < P.NumAdunits; j++)
                fprintf(dat, "\t%.10f", TimeSeries[i].incI_adunit[j]);
            for (j = 0; j < P.NumAdunits; j++)
                fprintf(dat, "\t%.10f", TimeSeries[i].incC_adunit[j]);
            for (j = 0; j < P.NumAdunits; j++)
                fprintf(dat, "\t%.10f", TimeSeries[i].incDC_adunit[j]);
            fprintf(dat, "\n");
        }
        fclose(dat);
    }
 
    if ((P.DoDigitalContactTracing) && (P.DoAdUnits) && (P.OutputDigitalContactTracing))
    {
        sprintf(outname, "%s.digitalcontacttracing.xls", OutFile); //modifying to csv file
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
            fprintf(dat, "t");
        for (i = 0; i < P.NumAdunits; i++)
        {
            fprintf(dat, "\tincDCT_%s", AdUnits[i].ad_name);
        }
        for (i = 0; i < P.NumAdunits; i++)
        {
            fprintf(dat, "\tDCT_%s", AdUnits[i].ad_name);
        }
        fprintf(dat, "\n");
        //print actual output
        for(i=0; i<P.NumSamples; i++)
        {
            fprintf(dat, "%.10lf", TimeSeries[i].t);
            for (j = 0; j < P.NumAdunits; j++)
            {
                fprintf(dat, "\t%.10lf", TimeSeries[i].incDCT_adunit[j]);
            }
            for (j = 0; j < P.NumAdunits; j++)
            {
                fprintf(dat, "\t%.10lf", TimeSeries[i].DCT_adunit[j]);
            }
        fprintf(dat, "\n");
        }
        fclose(dat);
 
    }
 
    if ((P.DoDigitalContactTracing) && (P.OutputDigitalContactDist))
    {
        sprintf(outname, "%s.digitalcontactdist.xls", OutFile); //modifying to csv file
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        //print headers
        fprintf(dat, "nContacts\tFrequency\n");
        for (i = 0; i < (MAX_CONTACTS + 1); i++)
        {
            fprintf(dat, "%i\t%i\n", i, State.contact_dist[i]);
        }
        fclose(dat);
    }
 
    if(P.KeyWorkerProphTimeStartBase < P.SampleTime)
        {
        sprintf(outname, "%s.keyworker.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t");
        for(i = 0; i < 2; i++) fprintf(dat, "\tI%i", i);
        for(i = 0; i < 2; i++) fprintf(dat, "\tC%i", i);
        for(i = 0; i < 2; i++) fprintf(dat, "\tT%i", i);
        fprintf(dat, "\t%i\t%i\n", P.KeyWorkerNum, P.KeyWorkerIncHouseNum);
        for(i = 0; i < P.NumSamples; i++)
            {
            fprintf(dat, "%.10f", TimeSeries[i].t);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", TimeSeries[i].incI_keyworker[j]);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", TimeSeries[i].incC_keyworker[j]);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", TimeSeries[i].cumT_keyworker[j]);
            fprintf(dat, "\n");
            }
        fclose(dat);
        }
 
    if(P.DoInfectionTree)
        {
        sprintf(outname, "%s.tree.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        for(i = 0; i < P.PopSize; i++)
            if(Hosts[i].infect_type % INFECT_TYPE_MASK > 0)
                fprintf(dat, "%i\t%i\t%i\t%i\n", i, Hosts[i].infector, Hosts[i].infect_type % INFECT_TYPE_MASK, (int)HOST_AGE_YEAR(i));
        fclose(dat);
        }
#if defined(_WIN32) || defined(IMAGE_MAGICK)
    static int dm[13] ={0,31,28,31,30,31,30,31,31,30,31,30,31};
    int d, m, y, dml, f;
#ifdef _WIN32
    //if(P.OutputBitmap == 1) CloseAvi(avi);
    //if((TimeSeries[P.NumSamples - 1].extinct) && (P.OutputOnlyNonExtinct))
    //  {
    //  sprintf(outname, "%s.ge" DIRECTORY_SEPARATOR "%s.avi", OutFile, OutFile);
    //  DeleteFile(outname);
    //  }
#endif
    if(P.OutputBitmap >= 1 && P.BitmapFormat == BF_PNG)
        {
        // Generate Google Earth .kml file
        sprintf(outname, "%s.ge" DIRECTORY_SEPARATOR "%s.ge.kml", OutFile, OutFile); //sprintf(outname,"%s.ge" DIRECTORY_SEPARATOR "%s.kml",OutFileBase,OutFile);
        if(!(dat = fopen(outname, "wb")))
            {
            ERR_CRITICAL("Unable to open output kml file\n");
            }
        fprintf(dat, "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<kml xmlns=\"http://earth.google.com/kml/2.2\">\n<Document>\n");
        fprintf(dat, "<name>%s</name>\n", OutFile);
        y = 2009;
        m = 1;
        d = 1;
        for(i = 0; i < P.NumSamples; i++)
            {
            fprintf(dat, "<GroundOverlay>\n<name>Snapshot %i</name>\n", i + 1);
            fprintf(dat, "<TimeSpan>\n<begin>%i-%02i-%02iT00:00:00Z</begin>\n", y, m, d);
            d += (int)P.SampleStep; // SampleStep has to be an integer here.
            do
                {
                f = 1;
                dml = dm[m];
                if((m == 2) && (y % 4 == 0)) dml = 29;
                if(d > dml)
                    {
                    m++;
                    if(m > 12)
                        {
                        m -= 12;
                        y++;
                        }
                    d -= dml;
                    f = 0;
                    }
                } while(!f);
                fprintf(dat, "<end>%i-%02i-%02iT00:00:00Z</end>\n</TimeSpan>\n", y, m, d);
                sprintf(outname, "%s.ge" DIRECTORY_SEPARATOR "%s.%i.png", OutFile, OutFile, i + 1);
                fprintf(dat, "<Icon>\n<href>%s</href>\n</Icon>\n", outname);
                fprintf(dat, "<LatLonBox>\n<north>%.10f</north>\n<south>%.10f</south>\n<east>%.10f</east>\n<west>%.10f</west>\n</LatLonBox>\n",
                    P.SpatialBoundingBox[3], P.SpatialBoundingBox[1], P.SpatialBoundingBox[2], P.SpatialBoundingBox[0]);
                fprintf(dat, "</GroundOverlay>\n");
            }
        fprintf(dat, "</Document>\n</kml>\n");
        fclose(dat);
        }
#endif
 
 
    if(P.DoSeverity)
    {
        sprintf(outname, "%s.severity.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open severity output file\n");
        fprintf(dat, "t\tS\tI\tR\tincI\tMild\tILI\tSARI\tCritical\tCritRecov\tincMild\tincILI\tincSARI\tincCritical\tincCritRecov\tincDeath\tincDeath_ILI\tincDeath_SARI\tincDeath_Critical\tcumMild\tcumILI\tcumSARI\tcumCritical\tcumCritRecov\tcumDeath\tcumDeath_ILI\tcumDeath_SARI\tcumDeath_Critical\n");//\t\t%.10f\t%.10f\t%.10f\n",P.R0household,P.R0places,P.R0spatial);
        for (i = 0; i < P.NumSamples; i++)
        {
            fprintf(dat, "%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\n",
                TimeSeries[i].t, TimeSeries[i].S, TimeSeries[i].I, TimeSeries[i].R, TimeSeries[i].incI,
                TimeSeries[i].Mild      , TimeSeries[i].ILI     , TimeSeries[i].SARI    , TimeSeries[i].Critical    , TimeSeries[i].CritRecov   ,
                TimeSeries[i].incMild   , TimeSeries[i].incILI  , TimeSeries[i].incSARI , TimeSeries[i].incCritical , TimeSeries[i].incCritRecov,
                TimeSeries[i].incD, TimeSeries[i].incDeath_ILI, TimeSeries[i].incDeath_SARI, TimeSeries[i].incDeath_Critical,
                TimeSeries[i].cumMild   , TimeSeries[i].cumILI  , TimeSeries[i].cumSARI , TimeSeries[i].cumCritical , TimeSeries[i].cumCritRecov, TimeSeries[i].D   ,
                TimeSeries[i].cumDeath_ILI, TimeSeries[i].cumDeath_SARI, TimeSeries[i].cumDeath_Critical);
        }
        fclose(dat);
 
        if((P.DoAdUnits) && (P.OutputSeverityAdminUnit))
        {
            sprintf(outname, "%s.severity.adunit.xls", OutFile);
            if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
            fprintf(dat, "t");

            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tMild_%s"                 , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tILI_%s"                  , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tSARI_%s"                 , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tCritical_%s"             , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tCritRecov_%s"            , AdUnits[i].ad_name);

            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincI_%s"                 , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincMild_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincILI_%s"               , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincSARI_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincCritical_%s"          , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincCritRecov_%s"         , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath_adu%s"          , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath_ILI_adu%s"      , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath_SARI_adu%s"     , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath_Critical_adu%s" , AdUnits[i].ad_name);

            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumMild_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumILI_%s"               , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumSARI_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumCritical_%s"          , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumCritRecov_%s"         , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeaths_%s"            , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeath_ILI_%s"         , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeath_SARI_%s"        , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeath_Critical_%s"    , AdUnits[i].ad_name);
 
            fprintf(dat, "\n");

            for(i = 0; i < P.NumSamples; i++)
            {
                fprintf(dat, "%.10f", TimeSeries[i].t);

                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].Mild_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].ILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].SARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].Critical_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].CritRecov_adunit[j]);

                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incMild_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incSARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incCritical_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incCritRecov_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incD_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incDeath_ILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incDeath_SARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].incDeath_Critical_adunit[j]);

                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumMild_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumSARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumCritical_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumCritRecov_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumD_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumDeath_ILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumDeath_SARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", TimeSeries[i].cumDeath_Critical_adunit[j]);
 
                if(i != P.NumSamples - 1) fprintf(dat, "\n");
            }
            fclose(dat);
        }
    }
}
 
void SaveSummaryResults(void) 
{
    int i, j;
    double c, t;
    FILE* dat;
    char outname[1024];
 
    c = 1 / ((double)(P.NRactE + P.NRactNE));
 
    if (P.OutputNonSeverity)
    {
        sprintf(outname, "%s.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t\tS\tL\tI\tR\tD\tincI\tincR\tincD\tincC\tincDC\tincTC\tincH\tcumT\tcumTmax\tcumTP\tcumV\tcumVmax\tExtinct\trmsRad\tmaxRad\tvS\tvI\tvR\tvD\tvincI\tvincR\tvincFC\tvincC\tvincDC\tvincTC\tvincH\tvrmsRad\tvmaxRad\t\t%i\t%i\t%.10f\t%.10f\t%.10f\t\t%.10f\t%.10f\t%.10f\t%.10f\n",
            P.NRactNE, P.NRactE, P.R0household, P.R0places, P.R0spatial, c * PeakHeightSum, c * PeakHeightSS - c * c * PeakHeightSum * PeakHeightSum, c * PeakTimeSum, c * PeakTimeSS - c * c * PeakTimeSum * PeakTimeSum);
        c = 1 / ((double)P.NRactual);

        for(i = 0; i < P.NumSamples; i++)
        {
            fprintf(dat, "%.10f\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t%10lf\t",
                c * TSMean[i].t, c * TSMean[i].S, c * TSMean[i].L, c * TSMean[i].I, c * TSMean[i].R,
                c * TSMean[i].D, c * TSMean[i].incI, c * TSMean[i].incR, c * TSMean[i].incFC, c * TSMean[i].incC, c * TSMean[i].incDC, c * TSMean[i].incTC, c * TSMean[i].incH,
                c * TSMean[i].cumT, TSMean[i].cumTmax, c * TSMean[i].cumTP, c * TSMean[i].cumV, TSMean[i].cumVmax, c * TSMean[i].extinct, c * TSMean[i].rmsRad, c * TSMean[i].maxRad);
            fprintf(dat, "%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\n",
                c * TSVar[i].S      - c * c * TSMean[i].S       * TSMean[i].S,
                c * TSVar[i].I      - c * c * TSMean[i].I       * TSMean[i].I,
                c * TSVar[i].R      - c * c * TSMean[i].R       * TSMean[i].R,
                c * TSVar[i].D      - c * c * TSMean[i].D       * TSMean[i].D,
                c * TSVar[i].incI   - c * c * TSMean[i].incI    * TSMean[i].incI,
                c * TSVar[i].incR   - c * c * TSMean[i].incR    * TSMean[i].incR,
                c * TSVar[i].incD   - c * c * TSMean[i].incD    * TSMean[i].incD,
                c * TSVar[i].incC   - c * c * TSMean[i].incC    * TSMean[i].incC,
                c * TSVar[i].incDC  - c * c * TSMean[i].incDC   * TSMean[i].incDC, //added detected cases
                c * TSVar[i].incTC  - c * c * TSMean[i].incTC   * TSMean[i].incTC,
                c * TSVar[i].incH   - c * c * TSMean[i].incH    * TSMean[i].incH, //added hospitalisation
                c * TSVar[i].rmsRad - c * c * TSMean[i].rmsRad  * TSMean[i].rmsRad,
                c * TSVar[i].maxRad - c * c * TSMean[i].maxRad  * TSMean[i].maxRad);
        }
        fclose(dat);
    }
 
    if (P.OutputControls)
    {
        sprintf(outname, "%s.controls.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t\tS\tincC\tincTC\tincFC\tincH\tcumT\tcumUT\tcumTP\tcumV\tincHQ\tincAC\tincAH\tincAA\tincACS\tincAPC\tincAPA\tincAPCS\tpropSocDist");
        for(j = 0; j < NUM_PLACE_TYPES; j++) fprintf(dat, "\tprClosed_%i", j);
        fprintf(dat, "t\tvS\tvincC\tvincTC\tvincFC\tvincH\tvcumT\tvcumUT\tvcumTP\tvcumV");
        for(j = 0; j < NUM_PLACE_TYPES; j++) fprintf(dat, "\tvprClosed_%i", j);
        fprintf(dat, "\n");
        for(i = 0; i < P.NumSamples; i++)
            {
            fprintf(dat, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
                c * TSMean[i].t, c * TSMean[i].S, c * TSMean[i].incC, c * TSMean[i].incTC, c * TSMean[i].incFC, c * TSMean[i].incH,
                c * TSMean[i].cumT, c * TSMean[i].cumUT, c * TSMean[i].cumTP, c * TSMean[i].cumV, c * TSMean[i].incHQ,
                c * TSMean[i].incAC, c * TSMean[i].incAH, c * TSMean[i].incAA, c * TSMean[i].incACS,
                c * TSMean[i].incAPC, c * TSMean[i].incAPA, c * TSMean[i].incAPCS,c*TSMean[i].PropSocDist);
            for(j = 0; j < NUM_PLACE_TYPES; j++) fprintf(dat, "\t%lf", c * TSMean[i].PropPlacesClosed[j]);
            fprintf(dat, "\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf",
                c * TSVar[i].S - c * c * TSMean[i].S * TSMean[i].S,
                c * TSVar[i].incC - c * c * TSMean[i].incC * TSMean[i].incC,
                c * TSVar[i].incTC - c * c * TSMean[i].incTC * TSMean[i].incTC,
                c * TSVar[i].incFC - c * c * TSMean[i].incFC * TSMean[i].incFC,
                c * TSVar[i].incH - c * c * TSMean[i].incH * TSMean[i].incH,
                c * TSVar[i].cumT - c * c * TSMean[i].cumT * TSMean[i].cumT,
                c * TSVar[i].cumUT - c * c * TSMean[i].cumUT * TSMean[i].cumUT,
                c * TSVar[i].cumTP - c * c * TSMean[i].cumTP * TSMean[i].cumTP,
                c * TSVar[i].cumV - c * c * TSMean[i].cumV * TSMean[i].cumV);
            for(j = 0; j < NUM_PLACE_TYPES; j++) fprintf(dat, "\t%lf", TSVar[i].PropPlacesClosed[j]);
            fprintf(dat, "\n");
            }
        fclose(dat);
 
    }
 
    if (P.OutputAge)
    {
        sprintf(outname, "%s.age.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t");
        for(i = 0; i < NUM_AGE_GROUPS; i++)
            fprintf(dat, "\tI%i-%i", AGE_GROUP_WIDTH * i, AGE_GROUP_WIDTH * (i + 1));
        for(i = 0; i < NUM_AGE_GROUPS; i++)
            fprintf(dat, "\tC%i-%i", AGE_GROUP_WIDTH * i, AGE_GROUP_WIDTH * (i + 1));
        for(i = 0; i < NUM_AGE_GROUPS; i++)
            fprintf(dat, "\tD%i-%i", AGE_GROUP_WIDTH * i, AGE_GROUP_WIDTH * (i + 1));
        fprintf(dat, "\n");
        for(i = 0; i < P.NumSamples; i++)
            {
            fprintf(dat, "%.10f", c * TSMean[i].t);
            for(j = 0; j < NUM_AGE_GROUPS; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incIa[j]);
            for(j = 0; j < NUM_AGE_GROUPS; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incCa[j]);
            for(j = 0; j < NUM_AGE_GROUPS; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incDa[j]);
            fprintf(dat, "\n");
            }
        fprintf(dat, "dist");
        for(j = 0; j < NUM_AGE_GROUPS; j++)
            fprintf(dat, "\t%.10f", AgeDist[j]);
        fprintf(dat, "\n");
        fclose(dat);
    }
 
    if((P.DoAdUnits) && (P.DoAdunitOutput))
    {
        sprintf(outname, "%s.adunit.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t");
        for(i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tI_%s", AdUnits[i].ad_name);
        for(i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tC_%s", AdUnits[i].ad_name);
        for(i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tDC_%s", AdUnits[i].ad_name); //added detected cases: ggilani 03/02/15
        for(i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tT_%s", AdUnits[i].ad_name);
        for(i = 0; i < P.NumAdunits; i++) fprintf(dat, "\t%.10f", P.PopByAdunit[i][0]);
        for(i = 0; i < P.NumAdunits; i++) fprintf(dat, "\t%.10f", P.PopByAdunit[i][1]);
        fprintf(dat, "\n");
        for(i = 0; i < P.NumSamples; i++)
        {
            fprintf(dat, "%.10f", c * TSMean[i].t);
            for(j = 0; j < P.NumAdunits; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incI_adunit[j]);
            for(j = 0; j < P.NumAdunits; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incC_adunit[j]);
            for(j = 0; j < P.NumAdunits; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incDC_adunit[j]); //added detected cases: ggilani 03/02/15
            for(j = 0; j < P.NumAdunits; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].cumT_adunit[j]);
            fprintf(dat, "\n");
        }
        fclose(dat);
 
        if (P.OutputAdUnitVar)
        {
            sprintf(outname, "%s.adunitVar.xls", OutFile);
            if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
            fprintf(dat, "t");
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tI_%s", AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tC_%s", AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tDC_%s", AdUnits[i].ad_name); //added detected cases: ggilani 03/02/15
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tT_%s", AdUnits[i].ad_name);
            fprintf(dat, "\n");
            for (i = 0; i < P.NumSamples; i++)
            {
                fprintf(dat, "%.10f", c * TSMean[i].t);
                for (j = 0; j < P.NumAdunits; j++)
                    fprintf(dat, "\t%.10f", c * TSVar[i].incI_adunit[j] - c * c * TSMean[i].incI_adunit[j] * TSMean[i].incI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)
                    fprintf(dat, "\t%.10f", c * TSVar[i].incC_adunit[j] - c * c * TSMean[i].incC_adunit[j] * TSMean[i].incC_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)
                    fprintf(dat, "\t%.10f", c * TSVar[i].incDC_adunit[j] - c * c * TSMean[i].incDC_adunit[j] * TSMean[i].incDC_adunit[j]); //added detected cases: ggilani 03/02/15
                for (j = 0; j < P.NumAdunits; j++)
                    fprintf(dat, "\t%.10f", c * TSVar[i].cumT_adunit[j] - c * c * TSMean[i].cumT_adunit[j] * TSMean[i].cumT_adunit[j]);
                fprintf(dat, "\n");
            }
            fclose(dat);
        }
    }
 
    if ((P.DoDigitalContactTracing) && (P.DoAdUnits) && (P.OutputDigitalContactTracing))
    {
        sprintf(outname, "%s.digitalcontacttracing.xls", OutFile);
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t");
        for (i = 0; i < P.NumAdunits; i++)
        {
            fprintf(dat, "\tincDCT_%s", AdUnits[i].ad_name); // //printing headers for inc per admin unit
        }
        for (i = 0; i < P.NumAdunits; i++)
        {
            fprintf(dat, "\tDCT_%s", AdUnits[i].ad_name); // //printing headers for prevalence of digital contact tracing per admin unit
        }
        fprintf(dat, "\n");
        //print actual output
        for (i = 0; i < P.NumSamples; i++)
        {
            fprintf(dat, "%.10lf", c* TSMean[i].t);
            for (j = 0; j < P.NumAdunits; j++)
            {
                fprintf(dat, "\t%.10lf", c * TSMean[i].incDCT_adunit[j]);
            }
            for (j = 0; j < P.NumAdunits; j++)
            {
                fprintf(dat, "\t%.10lf", c * TSMean[i].DCT_adunit[j]);
            }
            fprintf(dat, "\n");
        }
 
        fclose(dat);
 
    }
 
    if(P.KeyWorkerProphTimeStartBase < P.SampleTime)
    {
        sprintf(outname, "%s.keyworker.xls", OutFile);
        if(!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t");
        for(i = 0; i < 2; i++) fprintf(dat, "\tI%i", i);
        for(i = 0; i < 2; i++) fprintf(dat, "\tC%i", i);
        for(i = 0; i < 2; i++) fprintf(dat, "\tT%i", i);
        for(i = 0; i < 2; i++) fprintf(dat, "\tvI%i", i);
        for(i = 0; i < 2; i++) fprintf(dat, "\tvC%i", i);
        for(i = 0; i < 2; i++) fprintf(dat, "\tvT%i", i);
        fprintf(dat, "\t%i\t%i\n", P.KeyWorkerNum, P.KeyWorkerIncHouseNum);
        for(i = 0; i < P.NumSamples; i++)
            {
            fprintf(dat, "%.10f", c * TSMean[i].t);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incI_keyworker[j]);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].incC_keyworker[j]);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", c * TSMean[i].cumT_keyworker[j]);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", c * TSVar[i].incI_keyworker[j] - c * c * TSMean[i].incI_keyworker[j] * TSMean[i].incI_keyworker[j]);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", c * TSVar[i].incC_keyworker[j] - c * c * TSMean[i].incC_keyworker[j] * TSMean[i].incC_keyworker[j]);
            for(j = 0; j < 2; j++)
                fprintf(dat, "\t%.10f", c * TSVar[i].cumT_keyworker[j] - c * c * TSMean[i].cumT_keyworker[j] * TSMean[i].cumT_keyworker[j]);
            fprintf(dat, "\n");
            }
        fclose(dat);
    }
 
    if (P.OutputInfType)
    {
        sprintf(outname, "%s.inftype.xls", OutFile);
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        fprintf(dat, "t\tR");
        for (j = 0; j < INFECT_TYPE_MASK; j++) fprintf(dat, "\tRtype_%i", j);
        for (j = 0; j < INFECT_TYPE_MASK; j++) fprintf(dat, "\tincItype_%i", j);
        for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\tRage_%i", j);
        fprintf(dat, "\n");
        for (i = 0; i < P.NumSamples; i++)
        {
            fprintf(dat, "%lf\t%lf", c * TSMean[i].t, c * TSMean[i].Rdenom);
            for (j = 0; j < INFECT_TYPE_MASK; j++) fprintf(dat, "\t%lf", c * TSMean[i].Rtype[j]);
            for (j = 0; j < INFECT_TYPE_MASK; j++) fprintf(dat, "\t%lf", c * TSMean[i].incItype[j]);
            for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%lf", c * TSMean[i].Rage[j]);
            fprintf(dat, "\n");
        }
        fclose(dat);
    }
 
    if (P.OutputR0)
    {
        sprintf(outname, "%s.R0.xls", OutFile);
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        for (i = 0; i < MAX_SEC_REC; i++)
        {
            fprintf(dat, "%i", i);
            for (j = 0; j < MAX_GEN_REC; j++)
                fprintf(dat, "\t%.10f", c * indivR0_av[i][j]);
            fprintf(dat, "\n");
        }
        fclose(dat);
    }
 
    if (P.OutputHousehold)
    {
        sprintf(outname, "%s.household.xls", OutFile);
        for (i = 1; i <= MAX_HOUSEHOLD_SIZE; i++)
        {
            t = 0;
            for (j = 1; j <= MAX_HOUSEHOLD_SIZE; j++)
                t += inf_household_av[i][j];
            inf_household_av[i][0] = denom_household[i] / c - t;
        }
        for (i = 1; i <= MAX_HOUSEHOLD_SIZE; i++)
        {
            t = 0;
            for (j = 1; j <= MAX_HOUSEHOLD_SIZE; j++)
                t += case_household_av[i][j];
            case_household_av[i][0] = denom_household[i] / c - t;
        }
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        for (i = 1; i <= MAX_HOUSEHOLD_SIZE; i++)
            fprintf(dat, "\t%i", i);
        fprintf(dat, "\n");
        for (i = 0; i <= MAX_HOUSEHOLD_SIZE; i++)
        {
            fprintf(dat, "%i", i);
            for (j = 1; j <= MAX_HOUSEHOLD_SIZE; j++)
                fprintf(dat, "\t%.10f", inf_household_av[j][i] * c);
            fprintf(dat, "\n");
        }
        fprintf(dat, "\n");
        for (i = 1; i <= MAX_HOUSEHOLD_SIZE; i++)
            fprintf(dat, "\t%i", i);
        fprintf(dat, "\n");
        for (i = 0; i <= MAX_HOUSEHOLD_SIZE; i++)
        {
            fprintf(dat, "%i", i);
            for (j = 1; j <= MAX_HOUSEHOLD_SIZE; j++)
                fprintf(dat, "\t%.10f", case_household_av[j][i] * c);
            fprintf(dat, "\n");
        }
        fclose(dat);
    }
 
    if (P.OutputCountry)
    {
        sprintf(outname, "%s.country.xls", OutFile);
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
        for (i = 0; i < MAX_COUNTRIES; i++)
            fprintf(dat, "%i\t%.10f\t%.10f\n", i, infcountry_av[i] * c, infcountry_num[i] * c);
        fclose(dat);
    }
 
    if (P.DoSeverity)
    {
        sprintf(outname, "%s.severity.xls", OutFile);
 
        if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open severity output file\n");
        fprintf(dat, "t\tPropSocDist\tS\tI\tR\tincI\tincC\tMild\tILI\tSARI\tCritical\tCritRecov\tSARIP\tCriticalP\tCritRecovP\tincMild\tincILI\tincSARI\tincCritical\tincCritRecov\tincSARIP\tincCriticalP\tincCritRecovP\tincDeath\tincDeath_ILI\tincDeath_SARI\tincDeath_Critical\tcumMild\tcumILI\tcumSARI\tcumCritical\tcumCritRecov\tcumDeath\tcumDeath_ILI\tcumDeath_SARI\tcumDeath_Critical\t");
        fprintf(dat, "PropSocDist_v\tS_v\tI_v\tR_v\tincI_v\tincC_v\tMild_v\tILI_v\tSARI_v\tCritical_v\tCritRecov_v\tincMild_v\tincILI_v\tincSARI_v\tincCritical_v\tincCritRecov_v\tincDeath_v\tincDeath_ILI_v\tincDeath_SARI_v\tincDeath_Critical_v\tcumMild_v\tcumILI_v\tcumSARI_v\tcumCritical_v\tcumCritRecov_v\tcumDeath_v\tcumDeath_ILI_v\tcumDeath_SARI_v\tcumDeath_Critical_v\n");
        double SARI, Critical, CritRecov, incSARI, incCritical, incCritRecov, sc1, sc2,sc3,sc4; //this stuff corrects bed prevalence for exponentially distributed time to test results in hospital
        sc1 = (P.Mean_TimeToTest > 0) ? exp(-1.0 / P.Mean_TimeToTest) : 0.0;
        sc2 = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestOffset / P.Mean_TimeToTest) : 0.0;
        sc3 = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestCriticalOffset / P.Mean_TimeToTest) : 0.0;
        sc4 = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestCritRecovOffset / P.Mean_TimeToTest) : 0.0;
        incSARI = incCritical = incCritRecov = 0;
        for (i = 0; i < P.NumSamples; i++)
        {
            if (i > 0)
            {
                SARI = (TSMean[i].SARI - TSMean[i - 1].SARI) * sc2 + SARI * sc1;
                Critical = (TSMean[i].Critical - TSMean[i - 1].Critical) * sc3 + Critical * sc1;
                CritRecov = (TSMean[i].CritRecov - TSMean[i - 1].CritRecov) * sc4 + CritRecov * sc1;
                incSARI = TSMean[i].incSARI * (1.0 - sc2) + incSARI * sc1;
                incCritical = TSMean[i].incCritical * (1.0 - sc3) + incCritical * sc1;
                incCritRecov = TSMean[i].incCritRecov * (1.0 - sc4) + incCritRecov * sc1;
            }
            else
            {
                SARI = TSMean[i].SARI * sc2;
                Critical = TSMean[i].Critical * sc3;
                CritRecov = TSMean[i].CritRecov * sc4;
            }
 
            fprintf(dat, "%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t",
                c* TSMean[i].t, c* TSMean[i].PropSocDist, c* TSMean[i].S, c* TSMean[i].I, c* TSMean[i].R, c* TSMean[i].incI, c* TSMean[i].incC,
                c* TSMean[i].Mild, c* TSMean[i].ILI, c* TSMean[i].SARI,c* TSMean[i].Critical, c* TSMean[i].CritRecov,c* (TSMean[i].SARI - SARI), c* (TSMean[i].Critical - Critical), c* (TSMean[i].CritRecov - CritRecov),
                c * TSMean[i].incMild, c * TSMean[i].incILI, c * TSMean[i].incSARI, c * TSMean[i].incCritical, c * TSMean[i].incCritRecov, c * incSARI, c * incCritical, c * incCritRecov, c * TSMean[i].incD,
                c * TSMean[i].incDeath_ILI, c * TSMean[i].incDeath_SARI, c * TSMean[i].incDeath_Critical,
                c * TSMean[i].cumMild, c * TSMean[i].cumILI, c * TSMean[i].cumSARI, c * TSMean[i].cumCritical, c * TSMean[i].cumCritRecov, c*TSMean[i].D,
                c * TSMean[i].cumDeath_ILI, c * TSMean[i].cumDeath_SARI, c * TSMean[i].cumDeath_Critical);
            fprintf(dat, "%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\t%.10f\n",
                c* TSVar[i].PropSocDist- c * TSMean[i].PropSocDist* c * TSMean[i].PropSocDist,
                c* TSVar[i].S- c * TSMean[i].S* c * TSMean[i].S,
                c* TSVar[i].I- c * TSMean[i].I* c * TSMean[i].I,
                c* TSVar[i].R- c * TSMean[i].R* c * TSMean[i].R,
                c* TSVar[i].incI- c * TSMean[i].incI* c * TSMean[i].incI,
                c* TSVar[i].incC- c * TSMean[i].incC* c * TSMean[i].incC,
                c* TSVar[i].Mild- c * TSMean[i].Mild* c * TSMean[i].Mild,
                c* TSVar[i].ILI- c * TSMean[i].incILI* c * TSMean[i].incILI,
                c* TSVar[i].SARI- c * TSMean[i].SARI* c * TSMean[i].SARI,
                c* TSVar[i].Critical- c * TSMean[i].Critical* c * TSMean[i].Critical,
                c* TSVar[i].CritRecov- c * TSMean[i].CritRecov* c * TSMean[i].CritRecov,
                c* TSVar[i].incMild- c * TSMean[i].incMild* c * TSMean[i].incMild,
                c* TSVar[i].incILI- c * TSMean[i].incILI* c * TSMean[i].incILI,
                c* TSVar[i].incSARI- c * TSMean[i].incSARI* c * TSMean[i].incSARI,
                c* TSVar[i].incCritical- c * TSMean[i].incCritical* c * TSMean[i].incCritical,
                c* TSVar[i].incCritRecov- c * TSMean[i].incCritRecov* c * TSMean[i].incCritRecov,
                c* TSVar[i].incD- c * TSMean[i].incD* c * TSMean[i].incD,
                c* TSVar[i].incDeath_ILI- c * TSMean[i].incDeath_ILI* c * TSMean[i].incDeath_ILI,
                c* TSVar[i].incDeath_SARI- c * TSMean[i].incDeath_SARI* c * TSMean[i].incDeath_SARI,
                c* TSVar[i].incDeath_Critical- c * TSMean[i].incDeath_Critical* c * TSMean[i].incDeath_Critical,
                c* TSVar[i].cumMild- c * TSMean[i].cumMild* c * TSMean[i].cumMild,
                c* TSVar[i].cumILI- c * TSMean[i].cumILI* c * TSMean[i].cumILI,
                c* TSVar[i].cumSARI- c * TSMean[i].cumSARI* c * TSMean[i].cumSARI,
                c* TSVar[i].cumCritical- c * TSMean[i].cumCritical* c * TSMean[i].cumCritical,
                c* TSVar[i].cumCritRecov- c * TSMean[i].cumCritRecov* c * TSMean[i].cumCritRecov,
                c* TSVar[i].D- c * TSMean[i].D* c * TSMean[i].D,
                c* TSVar[i].cumDeath_ILI- c * TSMean[i].cumDeath_ILI* c * TSMean[i].cumDeath_ILI,
                c* TSVar[i].cumDeath_SARI- c * TSMean[i].cumDeath_SARI* c * TSMean[i].cumDeath_SARI,
                c* TSVar[i].cumDeath_Critical- c * TSMean[i].cumDeath_Critical* c * TSMean[i].cumDeath_Critical);
        }
        fclose(dat);
        if (P.OutputSeverityAge)
        {
            double* SARI_a, * Critical_a, * CritRecov_a, * incSARI_a, * incCritical_a, * incCritRecov_a, sc1a, sc2a, sc3a, sc4a; //this stuff corrects bed prevalence for exponentially distributed time to test results in hospital
 
            if (!(SARI_a = (double*)malloc(NUM_AGE_GROUPS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(Critical_a = (double*)malloc(NUM_AGE_GROUPS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(CritRecov_a = (double*)malloc(NUM_AGE_GROUPS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(incSARI_a = (double*)malloc(NUM_AGE_GROUPS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(incCritical_a = (double*)malloc(NUM_AGE_GROUPS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(incCritRecov_a = (double*)malloc(NUM_AGE_GROUPS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            sc1a = (P.Mean_TimeToTest > 0) ? exp(-1.0 / P.Mean_TimeToTest) : 0.0;
            sc2a = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestOffset / P.Mean_TimeToTest) : 0.0;
            sc3a = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestCriticalOffset / P.Mean_TimeToTest) : 0.0;
            sc4a = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestCritRecovOffset / P.Mean_TimeToTest) : 0.0;
            for (i = 0; i < NUM_AGE_GROUPS; i++) incSARI_a[i] = incCritical_a[i] = incCritRecov_a[i] = 0;
            sprintf(outname, "%s.severity.age.xls", OutFile);
            if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
            fprintf(dat, "t");

            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tMild_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tILI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tSARI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tCritical_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tCritRecov_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tSARIP_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tCriticalP_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tCritRecovP_%i", i);

            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincMild_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincILI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincSARI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincCritical_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincCritRecov_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincSARIP_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincCriticalP_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincCritRecovP_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincDeath_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincDeath_ILI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincDeath_SARI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tincDeath__Critical_%i", i);

            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumMild_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumILI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumSARI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumCritical_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumCritRecov_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumDeaths_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumDeaths_ILI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumDeaths_SARI_%i", i);
            for (i = 0; i < NUM_AGE_GROUPS; i++) fprintf(dat, "\tcumDeaths_Critical_%i", i);
 
            fprintf(dat, "\n");

            for (i = 0; i < P.NumSamples; i++)
            {
                for (j = 0; j < NUM_AGE_GROUPS; j++)
                {
                    if (i > 0)
                    {
                        SARI_a[j] = (TSMean[i].SARI_age[j] - TSMean[i - 1].SARI_age[j]) * sc2a + SARI_a[j] * sc1a;
                        Critical_a[j] = (TSMean[i].Critical_age[j] - TSMean[i - 1].Critical_age[j]) * sc3a + Critical_a[j] * sc1a;
                        CritRecov_a[j] = (TSMean[i].CritRecov_age[j] - TSMean[i - 1].CritRecov_age[j]) * sc4a + CritRecov_a[j] * sc1a;
                        incSARI_a[j] = TSMean[i].incSARI_age[j] * (1.0 - sc2a) + incSARI_a[j] * sc1a;
                        incCritical_a[j] = TSMean[i].incCritical_age[j] * (1.0 - sc3a) + incCritical_a[j] * sc1a;
                        incCritRecov_a[j] = TSMean[i].incCritRecov_age[j] * (1.0 - sc4a) + incCritRecov_a[j] * sc1a;
                    }
                    else
                    {
                        SARI_a[j] = TSMean[i].SARI_age[j] * sc2a;
                        Critical_a[j] = TSMean[i].Critical_age[j] * sc3a;
                        CritRecov_a[j] = TSMean[i].CritRecov_age[j] * sc4a;
                    }
                }
                fprintf(dat, "%.10f", c * TSMean[i].t);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].Mild_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].ILI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].SARI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].Critical_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].CritRecov_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * (TSMean[i].SARI_age[j] - SARI_a[j]));
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * (TSMean[i].Critical_age[j] - Critical_a[j]));
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * (TSMean[i].CritRecov_age[j] - CritRecov_a[j]));

                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incIa[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incMild_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incILI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incSARI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incCritical_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incCritRecov_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * incSARI_a[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * incCritical_a[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * incCritRecov_a[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incDa[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incDeath_ILI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incDeath_SARI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].incDeath_Critical_age[j]);

                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumMild_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumILI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumSARI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumCritical_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumCritRecov_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * (TSMean[i].cumDeath_ILI_age[j] + TSMean[i].cumDeath_SARI_age[j] + TSMean[i].cumDeath_Critical_age[j]));
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumDeath_ILI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumDeath_SARI_age[j]);
                for (j = 0; j < NUM_AGE_GROUPS; j++) fprintf(dat, "\t%.10f", c * TSMean[i].cumDeath_Critical_age[j]);
                fprintf(dat, "\n");
            }
            fclose(dat);
            free(SARI_a); free(Critical_a); free(CritRecov_a);
            free(incSARI_a); free(incCritical_a); free(incCritRecov_a);
        }
        if ((P.DoAdUnits) && (P.OutputSeverityAdminUnit))
        {
            double* SARI_a, * Critical_a, * CritRecov_a, * incSARI_a, * incCritical_a, * incCritRecov_a, sc1a, sc2a,sc3a,sc4a; //this stuff corrects bed prevalence for exponentially distributed time to test results in hospital
 
            if (!(SARI_a = (double*)malloc(MAX_ADUNITS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(Critical_a = (double*)malloc(MAX_ADUNITS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(CritRecov_a = (double*)malloc(MAX_ADUNITS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(incSARI_a = (double*)malloc(MAX_ADUNITS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(incCritical_a = (double*)malloc(MAX_ADUNITS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            if (!(incCritRecov_a = (double*)malloc(MAX_ADUNITS * sizeof(double)))) ERR_CRITICAL("Unable to allocate temp storage\n");
            sc1a = (P.Mean_TimeToTest > 0) ? exp(-1.0 / P.Mean_TimeToTest) : 0.0;
            sc2a = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestOffset / P.Mean_TimeToTest) : 0.0;
            sc3a = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestCriticalOffset / P.Mean_TimeToTest) : 0.0;
            sc4a = (P.Mean_TimeToTest > 0) ? exp(-P.Mean_TimeToTestCritRecovOffset / P.Mean_TimeToTest) : 0.0;
            for (i = 0; i < P.NumAdunits; i++) incSARI_a[i] = incCritical_a[i] = incCritRecov_a[i] = 0;
            sprintf(outname, "%s.severity.adunit.xls", OutFile);
            if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
            fprintf(dat, "t");

            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tMild_%s"                 , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tILI_%s"                  , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tSARI_%s"                 , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tCritical_%s"             , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tCritRecov_%s"            , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tSARIP_%s"                , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tCriticalP_%s"            , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tCritRecovP_%s"           , AdUnits[i].ad_name);

            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincI_%s"                 , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincMild_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincILI_%s"               , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincSARI_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincCritical_%s"          , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincCritRecov_%s"         , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincSARIP_%s"             , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincCriticalP_%s"         , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincCritRecovP_%s"        , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath_%s"             , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath_ILI_%s"         , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath_SARI_%s"        , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tincDeath__Critical_%s"   , AdUnits[i].ad_name);

            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumMild_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumILI_%s"               , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumSARI_%s"              , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumCritical_%s"          , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumCritRecov_%s"         , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeaths_%s"            , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeaths_ILI_%s"        , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeaths_SARI_%s"       , AdUnits[i].ad_name);
            for (i = 0; i < P.NumAdunits; i++) fprintf(dat, "\tcumDeaths_Critical_%s"   , AdUnits[i].ad_name);
 
            fprintf(dat, "\n");

            for (i = 0; i < P.NumSamples; i++)
            {
                for (j = 0; j < P.NumAdunits; j++)
                {
                    if (i > 0)
                    {
                        SARI_a[j] = (TSMean[i].SARI_adunit[j] - TSMean[i - 1].SARI_adunit[j]) * sc2a + SARI_a[j] * sc1a;
                        Critical_a[j] = (TSMean[i].Critical_adunit[j] - TSMean[i - 1].Critical_adunit[j]) * sc3a + Critical_a[j] * sc1a;
                        CritRecov_a[j] = (TSMean[i].CritRecov_adunit[j] - TSMean[i - 1].CritRecov_adunit[j]) * sc4a + CritRecov_a[j] * sc1a;
                        incSARI_a[j] = TSMean[i].incSARI_adunit[j] * (1.0 - sc2a) + incSARI_a[j] * sc1a;
                        incCritical_a[j] = TSMean[i].incCritical_adunit[j] * (1.0 - sc3a) + incCritical_a[j] * sc1a;
                        incCritRecov_a[j] = TSMean[i].incCritRecov_adunit[j] * (1.0 - sc4a) + incCritRecov_a[j] * sc1a;
                    }
                    else
                    {
                        SARI_a[j] = TSMean[i].SARI_adunit[j] * sc2a;
                        Critical_a[j] = TSMean[i].Critical_adunit[j] * sc3a;
                        CritRecov_a[j] = TSMean[i].CritRecov_adunit[j] * sc4a;
                    }
                }
                fprintf(dat, "%.10f", c*TSMean[i].t);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].Mild_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].ILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].SARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].Critical_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].CritRecov_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * (TSMean[i].SARI_adunit[j] - SARI_a[j]));
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * (TSMean[i].Critical_adunit[j] - Critical_a[j]));
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * (TSMean[i].CritRecov_adunit[j] - CritRecov_a[j]));

                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incMild_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incSARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incCritical_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incCritRecov_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * incSARI_a[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * incCritical_a[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * incCritRecov_a[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incD_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incDeath_ILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incDeath_SARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].incDeath_Critical_adunit[j]);

                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumMild_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumSARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumCritical_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumCritRecov_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumD_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumDeath_ILI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumDeath_SARI_adunit[j]);
                for (j = 0; j < P.NumAdunits; j++)      fprintf(dat, "\t%.10f", c * TSMean[i].cumDeath_Critical_adunit[j]);
 
                fprintf(dat, "\n");
            }
            fclose(dat);
            free(SARI_a); free(Critical_a); free(CritRecov_a);
            free(incSARI_a); free(incCritical_a); free(incCritRecov_a);
        }
    }
}
 
void SaveRandomSeeds(void)
{
    /* function: SaveRandomSeeds(void)
     *
     * Purpose: outputs the random seeds used for each run to a file
     * Parameter: none
     * Returns: none
     *
     * Author: ggilani, 09/03/17
     */
    FILE* dat;
    char outname[1024];
 
    sprintf(outname, "%s.seeds.xls", OutFile);
    if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
    fprintf(dat, "%i\t%i\n", P.nextRunSeed1, P.nextRunSeed2);
    fclose(dat);
}
 
void SaveEvents(void)
{
    /* function: SaveEvents(void)
     *
     * Purpose: outputs event log to a csv file if required
     * Parameters: none
     * Returns: none
     *
     * Author: ggilani, 15/10/2014
     */
    int i;
    FILE* dat;
    char outname[1024];
 
    sprintf(outname, "%s.infevents.xls", OutFile);
    if (!(dat = fopen(outname, "wb"))) ERR_CRITICAL("Unable to open output file\n");
    fprintf(dat, "type,t,thread,ind_infectee,cell_infectee,listpos_infectee,adunit_infectee,x_infectee,y_infectee,t_infector,ind_infector,cell_infector\n");
    for (i = 0; i < nEvents; i++)
    {
        fprintf(dat, "%i\t%.10f\t%i\t%i\t%i\t%i\t%i\t%.10f\t%.10f\t%.10f\t%i\t%i\n",
            InfEventLog[i].type, InfEventLog[i].t, InfEventLog[i].thread, InfEventLog[i].infectee_ind, InfEventLog[i].infectee_cell, InfEventLog[i].listpos, InfEventLog[i].infectee_adunit, InfEventLog[i].infectee_x, InfEventLog[i].infectee_y, InfEventLog[i].t_infector, InfEventLog[i].infector_ind, InfEventLog[i].infector_cell);
    }
    fclose(dat);
}
 
void LoadSnapshot(void)
{
    FILE* dat;
    int i, j, * CellMemberArray, * CellSuscMemberArray;
    int32_t l;
    long long CM_offset, CSM_offset;
    double t;
    int** Array_InvCDF;
    float* Array_tot_prob, ** Array_cum_trans, ** Array_max_trans;
 
    if (!(dat = fopen(SnapshotLoadFile, "rb"))) ERR_CRITICAL("Unable to open snapshot file\n");
    fprintf(stderr, "Loading snapshot.");
    if (!(Array_InvCDF = (int**)malloc(P.NCP * sizeof(int*)))) ERR_CRITICAL("Unable to allocate temp cell storage\n");
    if (!(Array_max_trans = (float**)malloc(P.NCP * sizeof(float*)))) ERR_CRITICAL("Unable to temp allocate cell storage\n");
    if (!(Array_cum_trans = (float**)malloc(P.NCP * sizeof(float*)))) ERR_CRITICAL("Unable to temp allocate cell storage\n");
    if (!(Array_tot_prob = (float*)malloc(P.NCP * sizeof(float)))) ERR_CRITICAL("Unable to temp allocate cell storage\n");
    for (i = 0; i < P.NCP; i++)
    {
        Array_InvCDF[i] = Cells[i].InvCDF;
        Array_max_trans[i] = Cells[i].max_trans;
        Array_cum_trans[i] = Cells[i].cum_trans;
        Array_tot_prob[i] = Cells[i].tot_prob;
    }
 
    fread_big((void*)& i, sizeof(int), 1, dat); if (i != P.PopSize) ERR_CRITICAL_FMT("Incorrect N (%i %i) in snapshot file.\n", P.PopSize, i);
    fread_big((void*)& i, sizeof(int), 1, dat); if (i != P.NH) ERR_CRITICAL("Incorrect NH in snapshot file.\n");
    fread_big((void*)&i, sizeof(int), 1, dat); if (i != P.NC) ERR_CRITICAL_FMT("## %i neq %i\nIncorrect NC in snapshot file.", i, P.NC);
    fread_big((void*)& i, sizeof(int), 1, dat); if (i != P.NCP) ERR_CRITICAL("Incorrect NCP in snapshot file.\n");
    fread_big((void*)& i, sizeof(int), 1, dat); if (i != P.ncw) ERR_CRITICAL("Incorrect ncw in snapshot file.\n");
    fread_big((void*)& i, sizeof(int), 1, dat); if (i != P.nch) ERR_CRITICAL("Incorrect nch in snapshot file.\n");
    fread_big((void*)& l, sizeof(int32_t), 1, dat); if (l != P.setupSeed1) ERR_CRITICAL("Incorrect setupSeed1 in snapshot file.\n");
    fread_big((void*)& l, sizeof(int32_t), 1, dat); if (l != P.setupSeed2) ERR_CRITICAL("Incorrect setupSeed2 in snapshot file.\n");
    fread_big((void*)& t, sizeof(double), 1, dat); if (t != P.TimeStep) ERR_CRITICAL("Incorrect TimeStep in snapshot file.\n");
    fread_big((void*) & (P.SnapshotLoadTime), sizeof(double), 1, dat);
    P.NumSamples = 1 + (int)ceil((P.SampleTime - P.SnapshotLoadTime) / P.SampleStep);
    fprintf(stderr, ".");
    fread_big((void*)& CellMemberArray, sizeof(int*), 1, dat);
    fprintf(stderr, ".");
    fread_big((void*)& CellSuscMemberArray, sizeof(int*), 1, dat);
    fprintf(stderr, ".");
    CM_offset = State.CellMemberArray - CellMemberArray;
    CSM_offset = State.CellSuscMemberArray - CellSuscMemberArray;
 
    fread_big((void*)Hosts, sizeof(Person), (size_t)P.PopSize, dat);
    fprintf(stderr, ".");
    fread_big((void*)Households, sizeof(Household), (size_t)P.NH, dat);
    fprintf(stderr, ".");
    fread_big((void*)Cells, sizeof(Cell), (size_t)P.NC, dat);
    fprintf(stderr, ".");
    fread_big((void*)Mcells, sizeof(Microcell), (size_t)P.NMC, dat);
    fprintf(stderr, ".");
    fread_big((void*)State.CellMemberArray, sizeof(int), (size_t)P.PopSize, dat);
    fprintf(stderr, ".");
    fread_big((void*)State.CellSuscMemberArray, sizeof(int), (size_t)P.PopSize, dat);
    fprintf(stderr, ".");
    for (i = 0; i < P.NC; i++)
    {
        if (Cells[i].n > 0)
        {
            Cells[i].members += CM_offset;
            Cells[i].susceptible += CSM_offset;
            Cells[i].latent += CSM_offset;
            Cells[i].infected += CSM_offset;
        }
        for (j = 0; j < MAX_INTERVENTION_TYPES; j++) Cells[i].CurInterv[j] = -1; // turn interventions off in loaded image
    }
    for (i = 0; i < P.NMC; i++)
        if (Mcells[i].n > 0)
            Mcells[i].members += CM_offset;
 
    for (i = 0; i < P.NCP; i++)
    {
        Cells[i].InvCDF = Array_InvCDF[i];
        Cells[i].max_trans = Array_max_trans[i];
        Cells[i].cum_trans = Array_cum_trans[i];
        Cells[i].tot_prob = Array_tot_prob[i];
    }
    free(Array_tot_prob);
    free(Array_cum_trans);
    free(Array_max_trans);
    free(Array_InvCDF);
    fprintf(stderr, "\n");
    fclose(dat);
}
 
void SaveSnapshot(void)
{
    FILE* dat;
    int i = 1;
 
    if (!(dat = fopen(SnapshotSaveFile, "wb"))) ERR_CRITICAL("Unable to open snapshot file\n");
 
    fwrite_big((void*) & (P.PopSize), sizeof(int), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.NH), sizeof(int), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.NC), sizeof(int), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.NCP), sizeof(int), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.ncw), sizeof(int), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.nch), sizeof(int), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.setupSeed1), sizeof(int32_t), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.setupSeed2), sizeof(int32_t), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.TimeStep), sizeof(double), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (P.SnapshotSaveTime), sizeof(double), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (State.CellMemberArray), sizeof(int*), 1, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*) & (State.CellSuscMemberArray), sizeof(int*), 1, dat);
    fprintf(stderr, "## %i\n", i++);
 
    fwrite_big((void*)Hosts, sizeof(Person), (size_t)P.PopSize, dat);
 
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*)Households, sizeof(Household), (size_t)P.NH, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*)Cells, sizeof(Cell), (size_t)P.NC, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*)Mcells, sizeof(Microcell), (size_t)P.NMC, dat);
    fprintf(stderr, "## %i\n", i++);
 
    fwrite_big((void*)State.CellMemberArray, sizeof(int), (size_t)P.PopSize, dat);
    fprintf(stderr, "## %i\n", i++);
    fwrite_big((void*)State.CellSuscMemberArray, sizeof(int), (size_t)P.PopSize, dat);
    fprintf(stderr, "## %i\n", i++);
 
    fclose(dat);
}
 
void UpdateProbs(int DoPlace)
{
    if (!DoPlace)
    {
#pragma omp parallel for schedule(static,500) default(none) \
            shared(P, CellLookup)
        for (int j = 0; j < P.NCP; j++)
        {
            CellLookup[j]->tot_prob = 0;
            CellLookup[j]->S0 = CellLookup[j]->S + CellLookup[j]->L + CellLookup[j]->I;
            if (P.DoDeath)
            {
                CellLookup[j]->S0 += CellLookup[j]->n / 5;
                if ((CellLookup[j]->n < 100) || (CellLookup[j]->S0 > CellLookup[j]->n)) CellLookup[j]->S0 = CellLookup[j]->n;
            }
        }
    }
    else
    {
#pragma omp parallel for schedule(static,500) default(none) \
            shared(P, CellLookup)
        for (int j = 0; j < P.NCP; j++)
        {
            CellLookup[j]->S0 = CellLookup[j]->S;
            CellLookup[j]->tot_prob = 0;
        }
    }
#pragma omp parallel for schedule(static,500) default(none) \
        shared(P, CellLookup)
    for (int j = 0; j < P.NCP; j++)
    {
        int m, k;
        float t;
        CellLookup[j]->cum_trans[0] = ((float)(CellLookup[0]->S0)) * CellLookup[j]->max_trans[0];
        t = ((float)CellLookup[0]->n) * CellLookup[j]->max_trans[0];
        for (m = 1; m < P.NCP; m++)
        {
                CellLookup[j]->cum_trans[m] = CellLookup[j]->cum_trans[m - 1] + ((float)(CellLookup[m]->S0)) * CellLookup[j]->max_trans[m];
                t += ((float)CellLookup[m]->n) * CellLookup[j]->max_trans[m];
        }
        CellLookup[j]->tot_prob = CellLookup[j]->cum_trans[P.NCP - 1];
        for (m = 0; m < P.NCP; m++)
            CellLookup[j]->cum_trans[m] /= CellLookup[j]->tot_prob;
        CellLookup[j]->tot_prob /= t;
        for (k = m = 0; k <= 1024; k++)
        {
            while (CellLookup[j]->cum_trans[m] * 1024 < ((float)k)) m++;
            CellLookup[j]->InvCDF[k] = m;
        }
    }
}
 
int ChooseTriggerVariableAndValue(int AdUnit)
{
    int VariableAndValue = 0;
    if (P.DoGlobalTriggers)
    {
        if (P.DoPerCapitaTriggers)
            VariableAndValue = (int)floor(((double)State.trigDC) * P.GlobalIncThreshPop / ((double)P.PopSize));
        else
            VariableAndValue = State.trigDC;
    }
    else if (P.DoAdminTriggers) VariableAndValue = State.trigDC_adunit[AdUnit];
    else VariableAndValue = INT_MAX; 
 
    return VariableAndValue;
}
double ChooseThreshold(int AdUnit, double WhichThreshold) 
{
    double Threshold = 0;
    if (P.DoGlobalTriggers) Threshold = WhichThreshold;
    else if (P.DoAdminTriggers)
    {
        if (P.DoPerCapitaTriggers)
            Threshold = (int)ceil(((double)(AdUnits[AdUnit].n * WhichThreshold)) / P.IncThreshPop);
        else
            Threshold = WhichThreshold;
    }
    return Threshold;
}
 
 
void UpdateEfficaciesAndComplianceProportions(double t)
{
    for (int ChangeTime = 0; ChangeTime < P.Num_SD_ChangeTimes; ChangeTime++)
        if (t == P.SD_ChangeTimes[ChangeTime])
        {
            P.SocDistHouseholdEffectCurrent = P.SD_HouseholdEffects_OverTime[ChangeTime];   
            P.SocDistSpatialEffectCurrent   = P.SD_SpatialEffects_OverTime  [ChangeTime];   
            for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                P.SocDistPlaceEffectCurrent[PlaceType] = P.SD_PlaceEffects_OverTime[ChangeTime][PlaceType]; 

            P.EnhancedSocDistHouseholdEffectCurrent = P.Enhanced_SD_HouseholdEffects_OverTime   [ChangeTime];   
            P.EnhancedSocDistSpatialEffectCurrent   = P.Enhanced_SD_SpatialEffects_OverTime     [ChangeTime];   
            for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                P.EnhancedSocDistPlaceEffectCurrent[PlaceType] = P.Enhanced_SD_PlaceEffects_OverTime[ChangeTime][PlaceType]; 
 
            P.SocDistCellIncThresh = P.SD_CellIncThresh_OverTime[ChangeTime];               
        }

    for (int ChangeTime = 0; ChangeTime < P.Num_CI_ChangeTimes; ChangeTime++)
        if (t == P.CI_ChangeTimes[ChangeTime])
        {
            P.CaseIsolationEffectiveness        = P.CI_SpatialAndPlaceEffects_OverTime  [ChangeTime]; 
            P.CaseIsolationHouseEffectiveness   = P.CI_HouseholdEffects_OverTime        [ChangeTime]; 
 
            P.CaseIsolationProp                 = P.CI_Prop_OverTime                    [ChangeTime]; 
            P.CaseIsolation_CellIncThresh       = P.CI_CellIncThresh_OverTime           [ChangeTime]; 
        }

    if (P.DoHouseholds)
        for (int ChangeTime = 0; ChangeTime < P.Num_HQ_ChangeTimes; ChangeTime++)
            if (t == P.HQ_ChangeTimes[ChangeTime])
            {
                P.HQuarantineSpatialEffect  = P.HQ_SpatialEffects_OverTime              [ChangeTime];               
                P.HQuarantineHouseEffect    = P.HQ_HouseholdEffects_OverTime            [ChangeTime];               
                for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                    P.HQuarantinePlaceEffect[PlaceType] = P.HQ_PlaceEffects_OverTime    [ChangeTime][PlaceType];    
 
                P.HQuarantinePropIndivCompliant = P.HQ_Individual_PropComply_OverTime   [ChangeTime]; 
                P.HQuarantinePropHouseCompliant = P.HQ_Household_PropComply_OverTime    [ChangeTime]; 
 
                P.HHQuar_CellIncThresh          = P.HQ_CellIncThresh_OverTime           [ChangeTime]; 
            }

    if (P.DoPlaces)
    {
        for (int ChangeTime = 0; ChangeTime < P.Num_PC_ChangeTimes; ChangeTime++)
            if (t == P.PC_ChangeTimes[ChangeTime])
            {
//              unsigned short int ts = (unsigned short int) (P.TimeStepsPerDay * t);
//              for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
//#pragma omp parallel for schedule(static,1)
//                  for (int ThreadNum = 0; ThreadNum < P.NumThreads; ThreadNum++)
//                      for (int PlaceNum = ThreadNum; PlaceNum < P.Nplace[PlaceType]; PlaceNum += P.NumThreads)
//                          DoPlaceOpen(PlaceType, PlaceNum, ts, ThreadNum);
 
                P.PlaceCloseSpatialRelContact   = P.PC_SpatialEffects_OverTime  [ChangeTime];               
                P.PlaceCloseHouseholdRelContact = P.PC_HouseholdEffects_OverTime[ChangeTime];               
                for (int PlaceType = 0; PlaceType < P.PlaceTypeNum; PlaceType++)
                {
                    P.PlaceCloseEffect[PlaceType] = P.PC_PlaceEffects_OverTime[ChangeTime][PlaceType];  
                    P.PlaceClosePropAttending[PlaceType] = P.PC_PropAttending_OverTime[ChangeTime][PlaceType];  
                }
 
                P.PlaceCloseIncTrig             = P.PC_IncThresh_OverTime       [ChangeTime];               
                P.PlaceCloseFracIncTrig         = P.PC_FracIncThresh_OverTime   [ChangeTime];               
                P.PlaceCloseCellIncThresh       = P.PC_CellIncThresh_OverTime   [ChangeTime];               
                P.PlaceCloseDuration            = P.PC_Durs_OverTime            [ChangeTime];                           
 

                if(P.PlaceCloseTimeStart<1e10) P.PlaceCloseTimeStart = t;
 
                // ensure that new duration doesn't go over next change time. Judgement call here - talk to Neil if this is what he wants.
                if ((ChangeTime < P.Num_PC_ChangeTimes - 1) && (P.PlaceCloseTimeStart + P.PlaceCloseDuration >= P.PC_ChangeTimes[ChangeTime + 1]))
                    P.PlaceCloseDuration = P.PC_ChangeTimes[ChangeTime + 1] - P.PC_ChangeTimes[ChangeTime]; // -1;
                //fprintf(stderr, "\nt=%lf, n=%i (%i)  PlaceCloseDuration = %lf  (%lf) \n", t, ChangeTime, P.Num_PC_ChangeTimes, P.PlaceCloseDuration, P.PC_ChangeTimes[ChangeTime+1]);
            }
    }

    for (int ChangeTime = 0; ChangeTime < P.Num_DCT_ChangeTimes; ChangeTime++)
        if (t == P.DCT_ChangeTimes[ChangeTime])
        {
            P.DCTCaseIsolationEffectiveness         = P.DCT_SpatialAndPlaceEffects_OverTime [ChangeTime];   
            P.DCTCaseIsolationHouseEffectiveness    = P.DCT_HouseholdEffects_OverTime       [ChangeTime];   
            P.ProportionDigitalContactsIsolate      = P.DCT_Prop_OverTime                   [ChangeTime];   
            P.MaxDigitalContactsToTrace             = P.DCT_MaxToTrace_OverTime             [ChangeTime];
        }
}
 
void RecordSample(double t, int n)
{
    int j, k, S, L, I, R, D, N, cumC, cumTC, cumI, cumR, cumD, cumDC, cumFC;
    int cumH; //add number of hospitalised, cumulative hospitalisation: ggilani 28/10/14
    int cumCT; //added cumulative number of contact traced: ggilani 15/06/17
    int cumCC; //added cumulative number of cases who are contacts: ggilani 28/05/2019
    int cumDCT; //added cumulative number of cases who are digitally contact traced: ggilani 11/03/20
    int cumHQ, cumAC, cumAH, cumAA, cumACS, cumAPC, cumAPA, cumAPCS, numPC, trigDC,trigAlert, trigAlertC;
    int cumC_country[MAX_COUNTRIES]; //add cumulative cases per country
    unsigned short int ts;
    double s,thr;

    int Mild, ILI, SARI, Critical, CritRecov, cumMild, cumILI, cumSARI, cumCritical, cumCritRecov, cumDeath_ILI, cumDeath_SARI, cumDeath_Critical;
 
    ts = (unsigned short int) (P.TimeStepsPerDay * t);

    S = L = I = R = D = cumI = cumC = cumDC = cumTC = cumFC = cumHQ = cumAC = cumAA = cumAH = cumACS = cumAPC = cumAPA = cumAPCS = cumD = cumH = cumCT = cumCC = cumDCT = 0;
    for (int i = 0; i < MAX_COUNTRIES; i++) cumC_country[i] = 0;
    if (P.DoSeverity)
        Mild = ILI = SARI = Critical = CritRecov = cumMild = cumILI = cumSARI = cumCritical = cumCritRecov = cumDeath_ILI = cumDeath_SARI = cumDeath_Critical = 0;
 
#pragma omp parallel for schedule(static,10000) reduction(+:S,L,I,R,D,cumTC) default(none) \
        shared(P, CellLookup)
    for (int i = 0; i < P.NCP; i++)
    {
        Cell* ct = CellLookup[i];
        S += (int)ct->S;
        L += (int)ct->L;
        I += (int)ct->I;
        R += (int)ct->R;
        D += (int)ct->D;
        cumTC += (int)ct->cumTC;
    }
    cumR = R;
    cumD = D;
    //cumD = 0;
    N = S + L + I + R + D;
    if (N != P.PopSize) fprintf(stderr, "## %i #\n", P.PopSize - N);
    State.sumRad2 = 0;
    for (j = 0; j < P.NumThreads; j++)
    {
        cumI += StateT[j].cumI;
        cumC += StateT[j].cumC;
        cumDC += StateT[j].cumDC;
        cumFC += StateT[j].cumFC;
        cumH += StateT[j].cumH; //added cumulative hospitalisation
        cumCT += StateT[j].cumCT; //added contact tracing
        cumCC += StateT[j].cumCC; //added cases who are contacts
        cumDCT += StateT[j].cumDCT; //added cases who are digitally contact traced
        State.sumRad2 += StateT[j].sumRad2;
        State.sumRad2 += StateT[j].sumRad2;
        cumHQ += StateT[j].cumHQ;
        cumAC += StateT[j].cumAC;
        cumAA += StateT[j].cumAA;
        cumAPC += StateT[j].cumAPC;
        cumAPA += StateT[j].cumAPA;
        cumAPCS += StateT[j].cumAPCS;
        cumAH += StateT[j].cumAH;
        cumACS += StateT[j].cumACS;
        //cumD += StateT[j].cumD;
 
        if (P.DoSeverity)
        {
            Mild                += StateT[j].Mild               ;
            ILI                 += StateT[j].ILI                ;
            SARI                += StateT[j].SARI               ;
            Critical            += StateT[j].Critical           ;
            CritRecov           += StateT[j].CritRecov          ;

            cumMild             += StateT[j].cumMild            ;
            cumILI              += StateT[j].cumILI             ;
            cumSARI             += StateT[j].cumSARI            ;
            cumCritical         += StateT[j].cumCritical        ;
            cumCritRecov        += StateT[j].cumCritRecov       ;
            cumDeath_ILI        += StateT[j].cumDeath_ILI       ;
            cumDeath_SARI       += StateT[j].cumDeath_SARI      ;
            cumDeath_Critical   += StateT[j].cumDeath_Critical  ;
        }
 
        //add up cumulative country counts: ggilani - 12/11/14
        for (int i = 0; i < MAX_COUNTRIES; i++) cumC_country[i] += StateT[j].cumC_country[i];
        if (State.maxRad2 < StateT[j].maxRad2) State.maxRad2 = StateT[j].maxRad2;
    }
    for (j = 0; j < P.NumThreads; j++)
        StateT[j].maxRad2 = State.maxRad2;
    TimeSeries[n].t = t;
    TimeSeries[n].S = (double)S;
    TimeSeries[n].L = (double)L;
    TimeSeries[n].I = (double)I;
    TimeSeries[n].R = (double)R;
    TimeSeries[n].D = (double)D;
    TimeSeries[n].incI = (double)(cumI - State.cumI);
    TimeSeries[n].incC = (double)(cumC - State.cumC);
    TimeSeries[n].incFC = (double)(cumFC - State.cumFC);
    TimeSeries[n].incH = (double)(cumH - State.cumH); //added incidence of hospitalisation
    TimeSeries[n].incCT = (double)(cumCT - State.cumCT); // added contact tracing
    TimeSeries[n].incCC = (double)(cumCC - State.cumCC); // added cases who are contacts
    TimeSeries[n].incDCT = (double)(cumDCT - State.cumDCT); //added cases who are digitally contact traced
    TimeSeries[n].incDC = (double)(cumDC - State.cumDC); //added incidence of detected cases
    TimeSeries[n].incTC = (double)(cumTC - State.cumTC);
    TimeSeries[n].incR = (double)(cumR - State.cumR);
    TimeSeries[n].incD = (double)(cumD - State.cumD);
    TimeSeries[n].incHQ = (double)(cumHQ - State.cumHQ);
    TimeSeries[n].incAC = (double)(cumAC - State.cumAC);
    TimeSeries[n].incAH = (double)(cumAH - State.cumAH);
    TimeSeries[n].incAA = (double)(cumAA - State.cumAA);
    TimeSeries[n].incACS = (double)(cumACS - State.cumACS);
    TimeSeries[n].incAPC = (double)(cumAPC - State.cumAPC);
    TimeSeries[n].incAPA = (double)(cumAPA - State.cumAPA);
    TimeSeries[n].incAPCS = (double)(cumAPCS - State.cumAPCS);
    TimeSeries[n].cumT = State.cumT;
    TimeSeries[n].cumUT = State.cumUT;
    TimeSeries[n].cumTP = State.cumTP;
    TimeSeries[n].cumV = State.cumV;
    TimeSeries[n].cumVG = State.cumVG; //added VG;
    TimeSeries[n].cumDC = cumDC;
    //fprintf(stderr, "\ncumD=%i last_cumD=%i incD=%lg\n ", cumD, State.cumD, TimeSeries[n].incD);
    //incidence per country
    for (int i = 0; i < MAX_COUNTRIES; i++) TimeSeries[n].incC_country[i] = (double)(cumC_country[i] - State.cumC_country[i]);
    if (P.DoICUTriggers)
    {
        trigDC = cumCritical;
        if (n >= P.TriggersSamplingInterval) trigDC -= (int)TimeSeries[n - P.TriggersSamplingInterval].cumCritical;
    }
    else
    {
        trigDC = cumDC;
        if (n >= P.TriggersSamplingInterval) trigDC -= (int)TimeSeries[n - P.TriggersSamplingInterval].cumDC;
    }
    State.trigDC = trigDC;

    State.S = S;
    State.L = L;
    State.I = I;
    State.R = R;
    State.D = D;
    State.cumI = cumI;
    State.cumDC = cumDC;
    State.cumTC = cumTC;
    State.cumFC = cumFC;
    State.cumH = cumH; //added cumulative hospitalisation
    State.cumCT = cumCT; //added cumulative contact tracing
    State.cumCC = cumCC; //added cumulative cases who are contacts
    State.cumDCT = cumDCT; //added cumulative cases who are digitally contact traced
    State.cumC = cumC;
    State.cumR = cumR;
    State.cumD = cumD;
    State.cumHQ = cumHQ;
    State.cumAC = cumAC;
    State.cumAH = cumAH;
    State.cumAA = cumAA;
    State.cumACS = cumACS;
    State.cumAPC = cumAPC;
    State.cumAPA = cumAPA;
    State.cumAPCS = cumAPCS;
 
    if (P.DoSeverity)
    {
        TimeSeries[n].incMild           = (double)(cumMild              - State.cumMild             );
        TimeSeries[n].incILI            = (double)(cumILI               - State.cumILI              );
        TimeSeries[n].incSARI           = (double)(cumSARI              - State.cumSARI             );
        TimeSeries[n].incCritical       = (double)(cumCritical          - State.cumCritical         );
        TimeSeries[n].incCritRecov      = (double)(cumCritRecov         - State.cumCritRecov        );
        TimeSeries[n].incDeath_ILI      = (double)(cumDeath_ILI         - State.cumDeath_ILI        );
        TimeSeries[n].incDeath_SARI     = (double)(cumDeath_SARI        - State.cumDeath_SARI       );
        TimeSeries[n].incDeath_Critical = (double)(cumDeath_Critical    - State.cumDeath_Critical   );

        State.Mild              = Mild              ;
        State.ILI               = ILI               ;
        State.SARI              = SARI              ;
        State.Critical          = Critical          ;
        State.CritRecov         = CritRecov         ;
        State.cumMild           = cumMild           ;
        State.cumILI            = cumILI            ;
        State.cumSARI           = cumSARI           ;
        State.cumCritical       = cumCritical       ;
        State.cumCritRecov      = cumCritRecov      ;
        State.cumDeath_ILI      = cumDeath_ILI      ;
        State.cumDeath_SARI     = cumDeath_SARI     ;
        State.cumDeath_Critical = cumDeath_Critical ;

        TimeSeries[n].Mild              = Mild              ;
        TimeSeries[n].ILI               = ILI               ;
        TimeSeries[n].SARI              = SARI              ;
        TimeSeries[n].Critical          = Critical          ;
        TimeSeries[n].CritRecov         = CritRecov         ;
        TimeSeries[n].cumMild           = cumMild           ;
        TimeSeries[n].cumILI            = cumILI            ;
        TimeSeries[n].cumSARI           = cumSARI           ;
        TimeSeries[n].cumCritical       = cumCritical       ;
        TimeSeries[n].cumCritRecov      = cumCritRecov      ;
        TimeSeries[n].cumDeath_ILI      = cumDeath_ILI      ;
        TimeSeries[n].cumDeath_SARI     = cumDeath_SARI     ;
        TimeSeries[n].cumDeath_Critical = cumDeath_Critical ;
 
        for (int i = 0; i < NUM_AGE_GROUPS; i++)
        {
            TimeSeries[n].incMild_age[i] = (double)(-State.cumMild_age[i]);
            TimeSeries[n].incILI_age[i] = (double)(-State.cumILI_age[i]);
            TimeSeries[n].incSARI_age[i] = (double)(-State.cumSARI_age[i]);
            TimeSeries[n].incCritical_age[i] = (double)(-State.cumCritical_age[i]);
            TimeSeries[n].incCritRecov_age[i] = (double)(-State.cumCritRecov_age[i]);
            TimeSeries[n].incDeath_ILI_age[i] = (double)(-State.cumDeath_ILI_age[i]);
            TimeSeries[n].incDeath_SARI_age[i] = (double)(-State.cumDeath_SARI_age[i]);
            TimeSeries[n].incDeath_Critical_age[i] = (double)(-State.cumDeath_Critical_age[i]);
 
            State.Mild_age[i] = 0;
            State.ILI_age[i] = 0;
            State.SARI_age[i] = 0;
            State.Critical_age[i] = 0;
            State.CritRecov_age[i] = 0;
            State.cumMild_age[i] = 0;
            State.cumILI_age[i] = 0;
            State.cumSARI_age[i] = 0;
            State.cumCritical_age[i] = 0;
            State.cumCritRecov_age[i] = 0;
            State.cumDeath_ILI_age[i] = 0;
            State.cumDeath_SARI_age[i] = 0;
            State.cumDeath_Critical_age[i] = 0;
 
            for (j = 0; j < P.NumThreads; j++)
            {
                State.Mild_age[i] += StateT[j].Mild_age[i];
                State.ILI_age[i] += StateT[j].ILI_age[i];
                State.SARI_age[i] += StateT[j].SARI_age[i];
                State.Critical_age[i] += StateT[j].Critical_age[i];
                State.CritRecov_age[i] += StateT[j].CritRecov_age[i];
                State.cumMild_age[i] += StateT[j].cumMild_age[i];
                State.cumILI_age[i] += StateT[j].cumILI_age[i];
                State.cumSARI_age[i] += StateT[j].cumSARI_age[i];
                State.cumCritical_age[i] += StateT[j].cumCritical_age[i];
                State.cumCritRecov_age[i] += StateT[j].cumCritRecov_age[i];
                State.cumDeath_ILI_age[i] += StateT[j].cumDeath_ILI_age[i];
                State.cumDeath_SARI_age[i] += StateT[j].cumDeath_SARI_age[i];
                State.cumDeath_Critical_age[i] += StateT[j].cumDeath_Critical_age[i];
            }

            TimeSeries[n].incMild_age[i] += (double)(State.cumMild_age[i]);
            TimeSeries[n].incILI_age[i] += (double)(State.cumILI_age[i]);
            TimeSeries[n].incSARI_age[i] += (double)(State.cumSARI_age[i]);
            TimeSeries[n].incCritical_age[i] += (double)(State.cumCritical_age[i]);
            TimeSeries[n].incCritRecov_age[i] += (double)(State.cumCritRecov_age[i]);
            TimeSeries[n].incDeath_ILI_age[i] += (double)(State.cumDeath_ILI_age[i]);
            TimeSeries[n].incDeath_SARI_age[i] += (double)(State.cumDeath_SARI_age[i]);
            TimeSeries[n].incDeath_Critical_age[i] += (double)(State.cumDeath_Critical_age[i]);

            TimeSeries[n].Mild_age[i] = State.Mild_age[i];
            TimeSeries[n].ILI_age[i] = State.ILI_age[i];
            TimeSeries[n].SARI_age[i] = State.SARI_age[i];
            TimeSeries[n].Critical_age[i] = State.Critical_age[i];
            TimeSeries[n].CritRecov_age[i] = State.CritRecov_age[i];
            TimeSeries[n].cumMild_age[i] = State.cumMild_age[i];
            TimeSeries[n].cumILI_age[i] = State.cumILI_age[i];
            TimeSeries[n].cumSARI_age[i] = State.cumSARI_age[i];
            TimeSeries[n].cumCritical_age[i] = State.cumCritical_age[i];
            TimeSeries[n].cumCritRecov_age[i] = State.cumCritRecov_age[i];
            TimeSeries[n].cumDeath_ILI_age[i] = State.cumDeath_ILI_age[i];
            TimeSeries[n].cumDeath_SARI_age[i] = State.cumDeath_SARI_age[i];
            TimeSeries[n].cumDeath_Critical_age[i] = State.cumDeath_Critical_age[i];
        }
        if (P.DoAdUnits)
            for (int i = 0; i <= P.NumAdunits; i++)
            {
                TimeSeries[n].incMild_adunit            [i] = (double)(-State.cumMild_adunit            [i]);
                TimeSeries[n].incILI_adunit             [i] = (double)(-State.cumILI_adunit             [i]);
                TimeSeries[n].incSARI_adunit            [i] = (double)(-State.cumSARI_adunit            [i]);
                TimeSeries[n].incCritical_adunit        [i] = (double)(-State.cumCritical_adunit        [i]);
                TimeSeries[n].incCritRecov_adunit       [i] = (double)(-State.cumCritRecov_adunit       [i]);
                TimeSeries[n].incD_adunit               [i] = (double)(-State.cumD_adunit               [i]);
                TimeSeries[n].incDeath_ILI_adunit       [i] = (double)(-State.cumDeath_ILI_adunit       [i]);
                TimeSeries[n].incDeath_SARI_adunit      [i] = (double)(-State.cumDeath_SARI_adunit      [i]);
                TimeSeries[n].incDeath_Critical_adunit  [i] = (double)(-State.cumDeath_Critical_adunit  [i]);

                State.Mild_adunit               [i] = 0;
                State.ILI_adunit                [i] = 0;
                State.SARI_adunit               [i] = 0;
                State.Critical_adunit           [i] = 0;
                State.CritRecov_adunit          [i] = 0;
                State.cumMild_adunit            [i] = 0;
                State.cumILI_adunit             [i] = 0;
                State.cumSARI_adunit            [i] = 0;
                State.cumCritical_adunit        [i] = 0;
                State.cumCritRecov_adunit       [i] = 0;
                State.cumD_adunit               [i] = 0;
                State.cumDeath_ILI_adunit       [i] = 0;
                State.cumDeath_SARI_adunit      [i] = 0;
                State.cumDeath_Critical_adunit  [i] = 0;
 
                for (j = 0; j < P.NumThreads; j++)
                {
                    State.Mild_adunit               [i] += StateT[j].Mild_adunit                [i];
                    State.ILI_adunit                [i] += StateT[j].ILI_adunit                 [i];
                    State.SARI_adunit               [i] += StateT[j].SARI_adunit                [i];
                    State.Critical_adunit           [i] += StateT[j].Critical_adunit            [i];
                    State.CritRecov_adunit          [i] += StateT[j].CritRecov_adunit           [i];
                    State.cumMild_adunit            [i] += StateT[j].cumMild_adunit             [i];
                    State.cumILI_adunit             [i] += StateT[j].cumILI_adunit              [i];
                    State.cumSARI_adunit            [i] += StateT[j].cumSARI_adunit             [i];
                    State.cumCritical_adunit        [i] += StateT[j].cumCritical_adunit         [i];
                    State.cumCritRecov_adunit       [i] += StateT[j].cumCritRecov_adunit        [i];
                    State.cumD_adunit               [i] += StateT[j].cumD_adunit                [i];
                    State.cumDeath_ILI_adunit       [i] += StateT[j].cumDeath_ILI_adunit        [i];
                    State.cumDeath_SARI_adunit      [i] += StateT[j].cumDeath_SARI_adunit       [i];
                    State.cumDeath_Critical_adunit  [i] += StateT[j].cumDeath_Critical_adunit   [i];
                }

                TimeSeries[n].incMild_adunit            [i] += (double)(State.cumMild_adunit            [i]);
                TimeSeries[n].incILI_adunit             [i] += (double)(State.cumILI_adunit             [i]);
                TimeSeries[n].incSARI_adunit            [i] += (double)(State.cumSARI_adunit            [i]);
                TimeSeries[n].incCritical_adunit        [i] += (double)(State.cumCritical_adunit        [i]);
                TimeSeries[n].incCritRecov_adunit       [i] += (double)(State.cumCritRecov_adunit       [i]);
                TimeSeries[n].incD_adunit               [i] += (double)(State.cumD_adunit               [i]);
                TimeSeries[n].incDeath_ILI_adunit       [i] += (double)(State.cumDeath_ILI_adunit       [i]);
                TimeSeries[n].incDeath_SARI_adunit      [i] += (double)(State.cumDeath_SARI_adunit      [i]);
                TimeSeries[n].incDeath_Critical_adunit  [i] += (double)(State.cumDeath_Critical_adunit  [i]);

                TimeSeries[n].Mild_adunit               [i] = State.Mild_adunit                 [i];
                TimeSeries[n].ILI_adunit                [i] = State.ILI_adunit                  [i];
                TimeSeries[n].SARI_adunit               [i] = State.SARI_adunit                 [i];
                TimeSeries[n].Critical_adunit           [i] = State.Critical_adunit             [i];
                TimeSeries[n].CritRecov_adunit          [i] = State.CritRecov_adunit            [i];
                TimeSeries[n].cumMild_adunit            [i] = State.cumMild_adunit              [i];
                TimeSeries[n].cumILI_adunit             [i] = State.cumILI_adunit               [i];
                TimeSeries[n].cumSARI_adunit            [i] = State.cumSARI_adunit              [i];
                TimeSeries[n].cumCritical_adunit        [i] = State.cumCritical_adunit          [i];
                TimeSeries[n].cumCritRecov_adunit       [i] = State.cumCritRecov_adunit         [i];
                TimeSeries[n].cumD_adunit               [i] = State.cumD_adunit                 [i];
                TimeSeries[n].cumDeath_ILI_adunit       [i] = State.cumDeath_ILI_adunit         [i];
                TimeSeries[n].cumDeath_SARI_adunit      [i] = State.cumDeath_SARI_adunit        [i];
                TimeSeries[n].cumDeath_Critical_adunit  [i] = State.cumDeath_Critical_adunit    [i];
            }
    }
 
    //update cumulative cases per country
    for (int i = 0; i < MAX_COUNTRIES; i++) State.cumC_country[i] = cumC_country[i];
    //update overall state variable for cumulative cases per adunit
 
    TimeSeries[n].rmsRad = (State.cumI > 0) ? sqrt(State.sumRad2 / ((double)State.cumI)) : 0;
    TimeSeries[n].maxRad = sqrt(State.maxRad2);
    TimeSeries[n].extinct = ((((P.SmallEpidemicCases >= 0) && (State.R <= P.SmallEpidemicCases)) || (P.SmallEpidemicCases < 0)) && (State.I + State.L == 0)) ? 1 : 0;
    for (int i = 0; i < NUM_AGE_GROUPS; i++)
    {
        TimeSeries[n].incCa[i] = TimeSeries[n].incIa[i] = TimeSeries[n].incDa[i] = 0;
        for (j = 0; j < P.NumThreads; j++)
        {
            TimeSeries[n].incCa[i] += (double)StateT[j].cumCa[i];
            TimeSeries[n].incIa[i] += (double)StateT[j].cumIa[i];
            TimeSeries[n].incDa[i] += (double)StateT[j].cumDa[i];
        }
    }
 
    for (int i = 0; i < 2; i++)
    {
        TimeSeries[n].incC_keyworker[i] = TimeSeries[n].incI_keyworker[i] = TimeSeries[n].cumT_keyworker[i] = 0;
        for (j = 0; j < P.NumThreads; j++)
        {
            TimeSeries[n].incC_keyworker[i] += (double)StateT[j].cumC_keyworker[i];
            TimeSeries[n].incI_keyworker[i] += (double)StateT[j].cumI_keyworker[i];
            TimeSeries[n].cumT_keyworker[i] += (double)StateT[j].cumT_keyworker[i];
            StateT[j].cumC_keyworker[i] = StateT[j].cumI_keyworker[i] = 0;
        }
    }
 
    for (int i = 0; i < INFECT_TYPE_MASK; i++)
    {
        TimeSeries[n].incItype[i] = 0;
        for (j = 0; j < P.NumThreads; j++)
        {
            TimeSeries[n].incItype[i] += (double)StateT[j].cumItype[i];
            StateT[j].cumItype[i] = 0;
        }
    }
    if (P.DoAdUnits)
        for (int i = 0; i <= P.NumAdunits; i++)
        {
            TimeSeries[n].incI_adunit[i] = TimeSeries[n].incC_adunit[i] = TimeSeries[n].cumT_adunit[i] = TimeSeries[n].incH_adunit[i] = TimeSeries[n].incDC_adunit[i] = TimeSeries[n].incCT_adunit[i] = TimeSeries[n].incDCT_adunit[i] =  0; //added detected cases: ggilani 03/02/15
            for (j = 0; j < P.NumThreads; j++)
            {
                TimeSeries[n].incI_adunit[i] += (double)StateT[j].cumI_adunit[i];
                TimeSeries[n].incC_adunit[i] += (double)StateT[j].cumC_adunit[i];
                TimeSeries[n].incDC_adunit[i] += (double)StateT[j].cumDC_adunit[i]; //added detected cases: ggilani 03/02/15
                TimeSeries[n].incH_adunit[i] += (double)StateT[j].cumH_adunit[i]; //added hospitalisation
                TimeSeries[n].incCT_adunit[i] += (double)StateT[j].cumCT_adunit[i]; //added contact tracing: ggilani 15/06/17
                TimeSeries[n].incCC_adunit[i] += (double)StateT[j].cumCC_adunit[i]; //added cases who are contacts: ggilani 28/05/2019
                TimeSeries[n].incDCT_adunit[i] += (double)StateT[j].cumDCT_adunit[i]; //added cases who are digitally contact traced: ggilani 11/03/20
                TimeSeries[n].cumT_adunit[i] += (double)StateT[j].cumT_adunit[i];
                State.cumC_adunit[i] += StateT[j].cumC_adunit[i];
                State.cumDC_adunit[i] += StateT[j].cumDC_adunit[i];
                StateT[j].cumI_adunit[i] = StateT[j].cumC_adunit[i] = StateT[j].cumH_adunit[i] = StateT[j].cumDC_adunit[i] = StateT[j].cumCT_adunit[i] = StateT[j].cumCC_adunit[i] = StateT[j].cumDCT_adunit[i] = 0; //added hospitalisation, detected cases, contact tracing: ggilani 03/02/15, 15/06/17
            }
            if (P.DoICUTriggers)
            {
                State.trigDC_adunit[i] += (int)TimeSeries[n].incCritical_adunit[i];
                if (n >= P.TriggersSamplingInterval) State.trigDC_adunit[i] -= (int)TimeSeries[n - P.TriggersSamplingInterval].incCritical_adunit[i];
            }
            else
            {
                State.trigDC_adunit[i] += (int)TimeSeries[n].incDC_adunit[i];
                if (n >= P.TriggersSamplingInterval) State.trigDC_adunit[i] -= (int)TimeSeries[n - P.TriggersSamplingInterval].incDC_adunit[i];
            }
        }
    if (P.DoDigitalContactTracing)
        for (int i = 0; i < P.NumAdunits; i++)
            TimeSeries[n].DCT_adunit[i] = (double)AdUnits[i].ndct; //added total numbers of contacts currently isolated due to digital contact tracing: ggilani 11/03/20
    if (P.DoPlaces)
        for (int i = 0; i < NUM_PLACE_TYPES; i++)
        {
            numPC = 0;
            for (j = 0; j < P.Nplace[i]; j++)
                if (PLACE_CLOSED(i, j)) numPC++;
            State.NumPlacesClosed[i] = numPC;
            TimeSeries[n].PropPlacesClosed[i] = ((double)numPC) / ((double)P.Nplace[i]);
        }
    for (int i = k = 0; i < P.NMC; i++) if (Mcells[i].socdist == 2) k++;
    TimeSeries[n].PropSocDist=((double)k)/((double)P.NMC);
 
    //update contact number distribution in State
    for (int i = 0; i < (MAX_CONTACTS+1); i++)
    {
        for (j = 0; j < P.NumThreads; j++)
        {
            State.contact_dist[i] += StateT[j].contact_dist[i];
            StateT[j].contact_dist[i] = 0;
        }
    }
 
    trigAlertC = State.cumDC;
    if (n >= P.PreControlClusterIdDuration) trigAlertC -= (int)TimeSeries[n - P.PreControlClusterIdDuration].cumDC;
 
    if (P.PreControlClusterIdUseDeaths)
    {
        trigAlert = (int)TimeSeries[n].D;
        if (n >= P.PreControlClusterIdDuration) trigAlert -= (int) TimeSeries[n - P.PreControlClusterIdDuration].D;
    }
    else
    {
        trigAlert = trigAlertC;
    }
 
    if(((!P.DoAlertTriggerAfterInterv) && (trigAlert >= P.PreControlClusterIdCaseThreshold)) || ((P.DoAlertTriggerAfterInterv) &&
        (((trigAlertC >= P.PreControlClusterIdCaseThreshold)&&(P.ModelCalibIteration<4)) || ((t>=P.PreIntervTime) && (P.ModelCalibIteration >= 4)))))
    {
        if((!P.StopCalibration)&&(!InterruptRun))
        {
            if (P.PreControlClusterIdTime == 0)
            {
                P.PreIntervTime = P.PreControlClusterIdTime = t;
                if (P.PreControlClusterIdCalTime >= 0)
                {
                    P.PreControlClusterIdHolOffset = P.PreControlClusterIdTime - P.PreIntervIdCalTime;
//                  fprintf(stderr, "@@## trigAlertC=%i P.PreControlClusterIdHolOffset=%lg \n",trigAlertC, P.PreControlClusterIdHolOffset);
                }
            }
            if ((P.PreControlClusterIdCalTime >= 0)&& (!P.DoAlertTriggerAfterInterv))
            {
                P.StopCalibration = 1;
                InterruptRun = 1;
            }
            if ((P.DoAlertTriggerAfterInterv) && (t == P.PreControlClusterIdTime + P.PreControlClusterIdCalTime - P.PreIntervIdCalTime))
            {
                if ((trigAlert > 0)&&(P.ModelCalibIteration<20))
                {
                    s = ((double)trigAlert)/((double)P.AlertTriggerAfterIntervThreshold);
                    thr = 1.1 / sqrt((double)P.AlertTriggerAfterIntervThreshold);
                    if (thr < 0.05) thr = 0.05;
                    fprintf(stderr, "\n** %i %lf %lf | %lg / %lg \t", P.ModelCalibIteration, t, P.PreControlClusterIdTime + P.PreControlClusterIdCalTime - P.PreIntervIdCalTime, P.PreControlClusterIdHolOffset,s);
                    fprintf(stderr, "| %i %i %i %i -> ", trigAlert, trigAlertC, P.AlertTriggerAfterIntervThreshold, P.PreControlClusterIdCaseThreshold);
                    if (P.ModelCalibIteration == 1)
                    {
                        if ((((s - 1.0) <= thr) && (s >= 1)) || (((1.0 - s) <= thr / 2) && (s < 1)))
                        {
                            P.ModelCalibIteration = 100;
                            P.StopCalibration = 1;
                            fprintf(stderr, "Calibration ended.\n");
                        }
                        else
                        {
                            s = pow(s, 0.95);
                            k = (int)(((double)P.PreControlClusterIdCaseThreshold) / s);
                            if (k > 0) P.PreControlClusterIdCaseThreshold = k;
                        }
                    }
                    else if ((P.ModelCalibIteration >= 3) && ((P.ModelCalibIteration) % 2 == 1))
                    {
                        if ((((s - 1.0) <= thr) && (s >= 1)) || (((1.0 - s) <= thr / 2) && (s < 1)))
                        {
                            P.ModelCalibIteration=100;
                            P.StopCalibration = 1;
                            fprintf(stderr, "Calibration ended.\n");
                        }
                        else if (s > 1)
                        {
                            P.PreIntervTime--;
                            P.PreControlClusterIdHolOffset--;
                        }
                        else if (s < 1)
                        {
                            P.PreIntervTime++;
                            P.PreControlClusterIdHolOffset++;
                        }
                    }
                    else if ((P.ModelCalibIteration >= 3) && ((P.ModelCalibIteration) % 2 == 0))
                    {
                        if ((((s - 1.0) <= thr) && (s >= 1)) || (((1.0 - s) <= thr / 2) && (s < 1)))
                        {
                            P.ModelCalibIteration = 100;
                            P.StopCalibration = 1;
                            fprintf(stderr, "Calibration ended.\n");
                        }
                        else
                            P.SeedingScaling /=pow(s, 0.5);
                    }
                    P.ModelCalibIteration++;
                    if(P.ModelCalibIteration<16) InterruptRun = 1;
                    fprintf(stderr, "%i : %lg\n", P.PreControlClusterIdCaseThreshold, P.SeedingScaling);
                }
                else
                {
                    P.StopCalibration = 1;
                    InterruptRun = 1;
                }
            }
        }
        P.ControlPropCasesId = P.PostAlertControlPropCasesId;
 
        if (P.VaryEfficaciesOverTime)
            UpdateEfficaciesAndComplianceProportions(t - P.PreIntervTime);
 
// changed to a define for speed (though always likely inlined anyway) and to avoid clang compiler warnings re double alignment
#define DO_OR_DONT_AMEND_START_TIME(X,Y) if(X>=1e10) X=Y;

        for (int i = 0; i < P.NumAdunits; i++)
            if (ChooseTriggerVariableAndValue(i) > ChooseThreshold(i, P.CaseIsolation_CellIncThresh)) 
                DO_OR_DONT_AMEND_START_TIME(AdUnits[i].CaseIsolationTimeStart, t + ((P.DoInterventionDelaysByAdUnit)?AdUnits[i].CaseIsolationDelay: P.CaseIsolationTimeStartBase))
        for (int i = 0; i < P.NumAdunits; i++)
            if (ChooseTriggerVariableAndValue(i) > ChooseThreshold(i, P.HHQuar_CellIncThresh)) 
                    DO_OR_DONT_AMEND_START_TIME(AdUnits[i].HQuarantineTimeStart, t + ((P.DoInterventionDelaysByAdUnit)?AdUnits[i].HQuarantineDelay: P.HQuarantineTimeStartBase));

        if (P.DoDigitalContactTracing)
            for (int i = 0; i < P.NumAdunits; i++)
                if (ChooseTriggerVariableAndValue(i) > ChooseThreshold(i, P.DigitalContactTracing_CellIncThresh)) 
                    DO_OR_DONT_AMEND_START_TIME(AdUnits[i].DigitalContactTracingTimeStart, t + ((P.DoInterventionDelaysByAdUnit)?AdUnits[i].DCTDelay: P.DigitalContactTracingTimeStartBase));
 
        if (P.DoGlobalTriggers)
        {
            int TriggerValue = ChooseTriggerVariableAndValue(0);
            if (TriggerValue >= ChooseThreshold(0, P.TreatCellIncThresh))
                DO_OR_DONT_AMEND_START_TIME((P.TreatTimeStart), t + P.TreatTimeStartBase);
            if (TriggerValue >= P.VaccCellIncThresh) DO_OR_DONT_AMEND_START_TIME(P.VaccTimeStart, t + P.VaccTimeStartBase);
            if (TriggerValue >= P.SocDistCellIncThresh)
            {
                DO_OR_DONT_AMEND_START_TIME(P.SocDistTimeStart, t + P.SocDistTimeStartBase);
                //added this for admin unit based intervention delays based on a global trigger: ggilani 17/03/20
                if (P.DoInterventionDelaysByAdUnit)
                    for (int i = 0; i < P.NumAdunits; i++)
                        DO_OR_DONT_AMEND_START_TIME(AdUnits[i].SocialDistanceTimeStart, t + AdUnits[i].SocialDistanceDelay);
            }
            if (TriggerValue >= P.PlaceCloseCellIncThresh)
            {
                DO_OR_DONT_AMEND_START_TIME(P.PlaceCloseTimeStart, t + P.PlaceCloseTimeStartBase);
                if (P.DoInterventionDelaysByAdUnit)
                    for (int i = 0; i < P.NumAdunits; i++)
                        DO_OR_DONT_AMEND_START_TIME(AdUnits[i].PlaceCloseTimeStart, t + AdUnits[i].PlaceCloseDelay);
            }
            if (TriggerValue >= P.MoveRestrCellIncThresh)
                DO_OR_DONT_AMEND_START_TIME(P.MoveRestrTimeStart, t + P.MoveRestrTimeStartBase);
            if (TriggerValue >= P.KeyWorkerProphCellIncThresh)
                DO_OR_DONT_AMEND_START_TIME(P.KeyWorkerProphTimeStart, t + P.KeyWorkerProphTimeStartBase);
        }
        else
        {
            DO_OR_DONT_AMEND_START_TIME(P.TreatTimeStart, t + P.TreatTimeStartBase);
            DO_OR_DONT_AMEND_START_TIME(P.VaccTimeStart , t + P.VaccTimeStartBase);
            DO_OR_DONT_AMEND_START_TIME(P.SocDistTimeStart, t + P.SocDistTimeStartBase);
            DO_OR_DONT_AMEND_START_TIME(P.PlaceCloseTimeStart, t + P.PlaceCloseTimeStartBase);
            DO_OR_DONT_AMEND_START_TIME(P.MoveRestrTimeStart, t + P.MoveRestrTimeStartBase);
            DO_OR_DONT_AMEND_START_TIME(P.KeyWorkerProphTimeStart, t + P.KeyWorkerProphTimeStartBase);
        }
        DO_OR_DONT_AMEND_START_TIME(P.AirportCloseTimeStart, t + P.AirportCloseTimeStartBase);
    }
    if ((P.PlaceCloseIndepThresh > 0) && (((double)State.cumDC) >= P.PlaceCloseIndepThresh))
        DO_OR_DONT_AMEND_START_TIME(P.PlaceCloseTimeStart, t + P.PlaceCloseTimeStartBase);
 
    if (t > P.SocDistTimeStart + P.SocDistChangeDelay)
    {
        P.SocDistDurationCurrent = P.SocDistDuration2;
        P.SocDistHouseholdEffectCurrent = P.SocDistHouseholdEffect2;
        P.SocDistSpatialEffectCurrent = P.SocDistSpatialEffect2;
        P.EnhancedSocDistHouseholdEffectCurrent = P.EnhancedSocDistHouseholdEffect2;
        P.EnhancedSocDistSpatialEffectCurrent = P.EnhancedSocDistSpatialEffect2;
        for (int i = 0; i < P.PlaceTypeNum; i++)
        {
            P.SocDistPlaceEffectCurrent[i] = P.SocDistPlaceEffect2[i];
            P.EnhancedSocDistPlaceEffectCurrent[i] = P.EnhancedSocDistPlaceEffect2[i];
        }
    }
    //fix to switch off first place closure after P.PlaceCloseDuration has elapsed, if there are no school or cell-based triggers set
    if (t == P.PlaceCloseTimeStart + P.PlaceCloseDuration)
    {
        P.PlaceCloseTimeStartPrevious = P.PlaceCloseTimeStart;
        if ((P.PlaceCloseIncTrig == 0) && (P.PlaceCloseFracIncTrig == 0) && (P.PlaceCloseCellIncThresh == 0)) P.PlaceCloseTimeStart = 9e9;
    }
 
    if (!P.VaryEfficaciesOverTime)
    {
        if ((P.PlaceCloseTimeStart2 > P.PlaceCloseTimeStartPrevious) && 
            (t >= P.PlaceCloseTimeStartPrevious + P.PlaceCloseDuration) &&  
            (t >= P.PlaceCloseTimeStartPrevious + P.PlaceCloseTimeStartBase2 - P.PlaceCloseTimeStartBase))  
        {
            fprintf(stderr, "\nSecond place closure period (t=%lg)\n", t);
            P.PlaceCloseTimeStartPrevious = P.PlaceCloseTimeStart2 = P.PlaceCloseTimeStart = t;
            P.PlaceCloseDuration = P.PlaceCloseDuration2;
            P.PlaceCloseIncTrig = P.PlaceCloseIncTrig2;
            P.PlaceCloseCellIncThresh = P.PlaceCloseCellIncThresh2;
        }
    }
 
    if (P.OutputBitmap >= 1)
    {
        TSMean = TSMeanNE; TSVar = TSVarNE;
        CaptureBitmap   ();
        OutputBitmap    (0);
    }
}
 
void RecordInfTypes(void)
{
    int i, j, k, l, lc, lc2, b, c, n, nf, i2;
    double* res, * res_av, * res_var, t, s;
 
    for (n = 0; n < P.NumSamples; n++)
    {
        for (i = 0; i < INFECT_TYPE_MASK; i++) TimeSeries[n].Rtype[i] = 0;
        for (i = 0; i < NUM_AGE_GROUPS; i++) TimeSeries[n].Rage[i] = 0;
        TimeSeries[n].Rdenom = 0;
    }
    for (i = 0; i < INFECT_TYPE_MASK; i++) inftype[i] = 0;
    for (i = 0; i < MAX_COUNTRIES; i++) infcountry[i] = 0;
    for (i = 0; i < MAX_SEC_REC; i++)
        for (j = 0; j < MAX_GEN_REC; j++)
            indivR0[i][j] = 0;
    for (i = 0; i <= MAX_HOUSEHOLD_SIZE; i++)
        for (j = 0; j <= MAX_HOUSEHOLD_SIZE; j++)
            inf_household[i][j] = case_household[i][j] = 0;
    for (b = 0; b < P.NC; b++)
        if ((Cells[b].S != Cells[b].n) || (Cells[b].R > 0))
            for (c = 0; c < Cells[b].n; c++)
                Hosts[Cells[b].members[c]].listpos = 0;
    //  for(b=0;b<P.NC;b++)
    //      if((Cells[b].S!=Cells[b].n)||(Cells[b].R>0))
    {
        j = k = l = lc = lc2 = 0; t = 1e10;
        //          for(c=0;c<Cells[b].n;c++)
        for (i = 0; i < P.PopSize; i++)
        {
            //              i=Cells[b].members[c];
            if (j == 0) j = k = Households[Hosts[i].hh].nh;
            if ((Hosts[i].inf != InfStat_Susceptible) && (Hosts[i].inf != InfStat_ImmuneAtStart))
            {
                if (Hosts[i].latent_time * P.TimeStep <= P.SampleTime)
                    TimeSeries[(int)(Hosts[i].latent_time * P.TimeStep / P.SampleStep)].Rdenom++;
                infcountry[Mcells[Hosts[i].mcell].country]++;
                if (abs(Hosts[i].inf) < InfStat_Recovered)
                    l = -1;
                else if (l >= 0)
                    l++;
                if ((l >= 0) && ((Hosts[i].inf == InfStat_RecoveredFromSymp) || (Hosts[i].inf == InfStat_Dead_WasSymp)))
                {
                    lc2++;
                    if (Hosts[i].latent_time * P.TimeStep <= t) // This convoluted logic is to pick up households where the index is symptomatic
                    {
                        lc = 1; t = Hosts[i].latent_time * P.TimeStep;
                    }
                }
                else if ((l > 0) && (Hosts[i].latent_time * P.TimeStep < t))
                {
                    lc = 0; t = Hosts[i].latent_time * P.TimeStep;
                }
                i2 = Hosts[i].infector;
                if (i2 >= 0)
                {
                    Hosts[i2].listpos++;
                    if (Hosts[i2].latent_time * P.TimeStep <= P.SampleTime)
                    {
                        TimeSeries[(int)(Hosts[i2].latent_time * P.TimeStep / P.SampleStep)].Rtype[Hosts[i].infect_type % INFECT_TYPE_MASK]++;
                        TimeSeries[(int)(Hosts[i2].latent_time * P.TimeStep / P.SampleStep)].Rage[HOST_AGE_GROUP(i)]++;
                    }
                }
            }
            inftype[Hosts[i].infect_type % INFECT_TYPE_MASK]++;
            j--;
            if (j == 0)
            {
                if (l < 0) l = 0;
                inf_household[k][l]++;
                case_household[k][lc2]++; //now recording total symptomatic cases, rather than infections conditional on symptomatic index
                l = lc = lc2 = 0; t = 1e10;
            }
        }
    }
    for (b = 0; b < P.NC; b++)
        if ((Cells[b].S != Cells[b].n) || (Cells[b].R > 0))
            for (c = 0; c < Cells[b].n; c++)
            {
                i = Cells[b].members[c];
                if ((abs(Hosts[i].inf) == InfStat_Recovered) || (abs(Hosts[i].inf) == InfStat_Dead))
                {
                    l = Hosts[i].infect_type / INFECT_TYPE_MASK;
                    if ((l < MAX_GEN_REC) && (Hosts[i].listpos < MAX_SEC_REC)) indivR0[Hosts[i].listpos][l]++;
                }
            }
    /*  if(!TimeSeries[P.NumSamples-1].extinct) */
    {
        for (i = 0; i < INFECT_TYPE_MASK; i++) inftype_av[i] += inftype[i];
        for (i = 0; i < MAX_COUNTRIES; i++)
        {
            infcountry_av[i] += infcountry[i];
            if (infcountry[i] > 0) infcountry_num[i]++;
        }
        for (i = 0; i < MAX_SEC_REC; i++)
            for (j = 0; j < MAX_GEN_REC; j++)
                indivR0_av[i][j] += indivR0[i][j];
        for (i = 0; i <= MAX_HOUSEHOLD_SIZE; i++)
            for (j = 0; j <= MAX_HOUSEHOLD_SIZE; j++)
            {
                inf_household_av[i][j] += inf_household[i][j];
                case_household_av[i][j] += case_household[i][j];
            }
    }
    k = (P.PreIntervIdCalTime>0)?((int) (P.PreIntervIdCalTime - P.PreControlClusterIdTime)):0;
    for (n = 0; n < P.NumSamples; n++)
    {
        TimeSeries[n].t += k;
        s = 0;
        if (TimeSeries[n].Rdenom == 0) TimeSeries[n].Rdenom = 1e-10;
        for (i = 0; i < NUM_AGE_GROUPS; i++)
            TimeSeries[n].Rage[i] /= TimeSeries[n].Rdenom;
        for (i = 0; i < INFECT_TYPE_MASK; i++)
            s += (TimeSeries[n].Rtype[i] /= TimeSeries[n].Rdenom);
        TimeSeries[n].Rdenom = s;
    }
    nf = sizeof(Results) / sizeof(double);
    if (!P.DoAdUnits) nf -= MAX_ADUNITS; // TODO: This still processes most of the AdUnit arrays; just not the last one
    fprintf(stderr, "extinct=%i (%i)\n", (int) TimeSeries[P.NumSamples - 1].extinct, P.NumSamples - 1);
    if (TimeSeries[P.NumSamples - 1].extinct)
    {
        TSMean = TSMeanE; TSVar = TSVarE; P.NRactE++;
    }
    else
    {
        TSMean = TSMeanNE; TSVar = TSVarNE; P.NRactNE++;
    }
    lc = -k;
    for (n = 0; n < P.NumSamples; n++)
    {
        if ((n + lc >= 0) && (n + lc < P.NumSamples))
        {
            if (s < TimeSeries[n + lc].incC) { s = TimeSeries[n + lc].incC; t = P.SampleStep * ((double)(n + lc)); }
            res = (double*)&TimeSeries[n + lc];
            res_av = (double*)&TSMean[n];
            res_var = (double*)&TSVar[n];
            for (i = 1 /* skip over `t` */; i < nf; i++)
            {
                res_av[i] += res[i];
                res_var[i] += res[i] * res[i];
            }
            if (TSMean[n].cumTmax < TimeSeries[n + lc].cumT) TSMean[n].cumTmax = TimeSeries[n + lc].cumT;
            if (TSMean[n].cumVmax < TimeSeries[n + lc].cumV) TSMean[n].cumVmax = TimeSeries[n + lc].cumV;
        }
        TSMean[n].t += ((double) n )* P.SampleStep;
    }
    PeakHeightSum += s;
    PeakHeightSS += s * s;
    PeakTimeSum += t;
    PeakTimeSS += t * t;
}
 
 
void CalcOriginDestMatrix_adunit()
{
 
#pragma omp parallel for schedule(static) default(none) \
        shared(P, Cells, CellLookup, Mcells, StateT)
    for (int tn = 0; tn < P.NumThreads; tn++)
    {
        for (int i = tn; i < P.NCP; i += P.NumThreads)
        {
            //reset pop density matrix to zero
            double pop_dens_from[MAX_ADUNITS] = {};
 
            //find index of cell from which flow travels
            ptrdiff_t cl_from = CellLookup[i] - Cells;
            ptrdiff_t cl_from_mcl = (cl_from / P.nch) * P.NMCL * P.get_number_of_micro_cells_high() + (cl_from % P.nch) * P.NMCL;
 
            //loop over microcells in these cells to find populations in each admin unit and so flows
            for (int k = 0; k < P.NMCL; k++)
            {
                for (int l = 0; l < P.NMCL; l++)
                {
                    //get index of microcell
                    ptrdiff_t mcl_from = cl_from_mcl + l + k * P.get_number_of_micro_cells_high();
                    if (Mcells[mcl_from].n > 0)
                    {
                        //get proportion of each population of cell that exists in each admin unit
                        pop_dens_from[Mcells[mcl_from].adunit] += (((double)Mcells[mcl_from].n) / ((double)Cells[cl_from].n));
                    }
                }
            }
 
            for (int j = i; j < P.NCP; j++)
            {
                //reset pop density matrix to zero
                double pop_dens_to[MAX_ADUNITS] = {};
 
                //find index of cell which flow travels to
                ptrdiff_t cl_to = CellLookup[j] - Cells;
                ptrdiff_t cl_to_mcl = (cl_to / P.nch) * P.NMCL * P.get_number_of_micro_cells_high() + (cl_to % P.nch) * P.NMCL;
                //calculate distance and kernel between the cells
                //total_flow=Cells[cl_from].max_trans[j]*Cells[cl_from].n*Cells[cl_to].n;
                double total_flow;
                if (j == 0)
                {
                    total_flow = Cells[cl_from].cum_trans[j] * Cells[cl_from].n;
                }
                else
                {
                    total_flow = (Cells[cl_from].cum_trans[j] - Cells[cl_from].cum_trans[j - 1]) * Cells[cl_from].n;
                }
 
                //loop over microcells within destination cell
                for (int m = 0; m < P.NMCL; m++)
                {
                    for (int p = 0; p < P.NMCL; p++)
                    {
                        //get index of microcell
                        ptrdiff_t mcl_to = cl_to_mcl + p + m * P.get_number_of_micro_cells_high();
                        if (Mcells[mcl_to].n > 0)
                        {
                            //get proportion of each population of cell that exists in each admin unit
                            pop_dens_to[Mcells[mcl_to].adunit] += (((double)Mcells[mcl_to].n) / ((double)Cells[cl_to].n));
                        }
                    }
                }
 
                for (int m = 0; m < P.NumAdunits; m++)
                {
                    for (int p = 0; p < P.NumAdunits; p++)
                    {
                        if (m != p)
                        {
                            double flow = total_flow * pop_dens_from[m] * pop_dens_to[p]; //updated to remove reference to cross-border flows: ggilani 26/03/20
                            StateT[tn].origin_dest[m][p] += flow;
                            StateT[tn].origin_dest[p][m] += flow;
                        }
                    }
                }
            }
        }
    }
 
    //Sum up flow between adunits across threads
    for (int i = 0; i < P.NumAdunits; i++)
    {
        for (int j = 0; j < P.NumAdunits; j++)
        {
            for (int k = 0; k < P.NumThreads; k++)
            {
                AdUnits[i].origin_dest[j] += StateT[k].origin_dest[i][j];
            }
        }
    }
}

int GetInputParameter (FILE* dat, FILE* dat2, const char* SItemName, const char* ItemType, void* ItemPtr, int NumItem, int NumItem2, int Offset)
{
    int FindFlag;
 
    FindFlag = GetInputParameter2(dat, dat2, SItemName, ItemType, ItemPtr, NumItem, NumItem2, Offset);
    if (!FindFlag)
    {
        ERR_CRITICAL_FMT("\nUnable to find parameter `%s' in input file. Aborting program...\n", SItemName);
    }
    return FindFlag;
}
int GetInputParameter2(FILE* dat, FILE* dat2, const char* SItemName, const char* ItemType, void* ItemPtr, int NumItem, int NumItem2, int Offset)
{
    int FindFlag = 0;
 
    if (dat2) FindFlag = GetInputParameter3(dat2, SItemName, ItemType, ItemPtr, NumItem, NumItem2, Offset);
    if (!FindFlag)
        FindFlag = GetInputParameter3(dat, SItemName, ItemType, ItemPtr, NumItem, NumItem2, Offset);
    return FindFlag;
}
 
/*
    Reads a string (as per fscanf %s).
    Returns true if it succeeds, false on EOF, and does not return on error.
*/
bool readString(const char* SItemName, FILE* dat, char *buf) {
    int r = fscanf(dat, "%s", buf);
    if(r == 1) {
        return true;
    } else if (r == EOF) {
        if(ferror(dat)) {
            ERR_CRITICAL_FMT("fscanf failed for %s: %s.\n", SItemName, strerror(errno));
        } else {
            // EOF
            return false;
        }
    } else {
        ERR_CRITICAL_FMT("Unexpected fscanf result %d for %s.\n", r, SItemName);
    }
}
 
int GetInputParameter3(FILE* dat, const char* SItemName, const char* ItemType, void* ItemPtr, int NumItem, int NumItem2, int Offset)
{
    char match[10000] = "", ReadItemName[10000] = "", ItemName[10000];
    int FindFlag = 0, EndString, CurPos, i, j, n;
 
    n = 0;
    fseek(dat, 0, 0);
    sprintf(ItemName, "[%s]", SItemName);
    while (!FindFlag)
    {
        if(!readString(SItemName, dat, match)) return 0;
        FindFlag = (!strncmp(match, ItemName, strlen(match)));
        if (FindFlag)
        {
            CurPos = ftell(dat);
            strcpy(ReadItemName, match);
            EndString = (match[strlen(match) - 1] == ']');
            while ((!EndString) && (FindFlag))
            {
                if(!readString(SItemName, dat, match)) return 0;
                strcat(ReadItemName, " ");
                strcat(ReadItemName, match);
                FindFlag = (!strncmp(ReadItemName, ItemName, strlen(ReadItemName)));
                EndString = (ReadItemName[strlen(ReadItemName) - 1] == ']');
            }
            if (!EndString)
            {
                fseek(dat, CurPos, 0);
                FindFlag = 0;
            }
        }
    }
    if (FindFlag)
    {
        FindFlag = 0;
        if (!strcmp(ItemType, "%lf"))   n = 1;
        else if (!strcmp(ItemType, "%i"))   n = 2;
        else if (!strcmp(ItemType, "%s"))   n = 3;
        if (NumItem2 < 2)
        {
            if (NumItem == 1)
            {
                if(fscanf(dat, "%s", match) != 1) { ERR_CRITICAL_FMT("fscanf failed for %s\n", SItemName); }
                if ((match[0] == '#') && (match[1] == '1'))
                {
                    FindFlag++;
                    if (n == 1)
                        * ((double*)ItemPtr) = P.clP1;
                    else if (n == 2)
                        * ((int*)ItemPtr) = (int)P.clP1;
                    else if (n == 3)
                        sscanf(match, "%s", (char*)ItemPtr);
                }
                else if ((match[0] == '#') && (match[1] == '2'))
                {
                    FindFlag++;
                    if (n == 1)
                        * ((double*)ItemPtr) = P.clP2;
                    else if (n == 2)
                        * ((int*)ItemPtr) = (int)P.clP2;
                    else if (n == 3)
                        sscanf(match, "%s", (char*)ItemPtr);
                }
                else if((match[0] == '#') && (match[1] == '3'))
                    {
                    FindFlag++;
                    if(n == 1)
                        * ((double*)ItemPtr) = P.clP3;
                    else if(n == 2)
                        * ((int*)ItemPtr) = (int)P.clP3;
                    else if(n == 3)
                        sscanf(match, "%s", (char*)ItemPtr);
                    }
                else if((match[0] == '#') && (match[1] == '4'))
                    {
                    FindFlag++;
                    if(n == 1)
                        * ((double*)ItemPtr) = P.clP4;
                    else if(n == 2)
                        * ((int*)ItemPtr) = (int)P.clP4;
                    else if(n == 3)
                        sscanf(match, "%s", (char*)ItemPtr);
                    }
                else if((match[0] == '#') && (match[1] == '5'))
                    {
                    FindFlag++;
                    if(n == 1)
                        * ((double*)ItemPtr) = P.clP5;
                    else if(n == 2)
                        * ((int*)ItemPtr) = (int)P.clP5;
                    else if(n == 3)
                        sscanf(match, "%s", (char*)ItemPtr);
                    }
                else if((match[0] == '#') && (match[1] == '6'))
                    {
                    FindFlag++;
                    if(n == 1)
                        * ((double*)ItemPtr) = P.clP6;
                    else if(n == 2)
                        * ((int*)ItemPtr) = (int)P.clP6;
                    else if(n == 3)
                        sscanf(match, "%s", (char*)ItemPtr);
                    }
                else if ((match[0] != '[') && (!feof(dat)))
                {
                    FindFlag++;
                    if (n == 1)
                        sscanf(match, "%lf", (double*)ItemPtr);
                    else if (n == 2)
                        sscanf(match, "%i", (int*)ItemPtr);
                    else if (n == 3)
                        sscanf(match, "%s", (char*)ItemPtr);
                }
            }
            else
            {
                for (CurPos = 0; CurPos < NumItem; CurPos++)
                {
                    if(fscanf(dat, "%s", match) != 1) { ERR_CRITICAL_FMT("fscanf failed for %s\n", SItemName); }
                    if ((match[0] != '[') && (!feof(dat)))
                    {
                        FindFlag++;
                        if (n == 1)
                            sscanf(match, "%lf", ((double*)ItemPtr) + CurPos + Offset);
                        else if (n == 2)
                            sscanf(match, "%i", ((int*)ItemPtr) + CurPos + Offset);
                        else if (n == 3)
                            sscanf(match, "%s", *(((char**)ItemPtr) + CurPos + Offset));
                    }
                    else
                        CurPos = NumItem;
                }
            }
        }
        else
        {
            for (j = 0; j < NumItem; j++)
            { //added these braces
                for (i = 0; i < NumItem2; i++)
                {
                    if(fscanf(dat, "%s", match) != 1) { ERR_CRITICAL_FMT("fscanf failed for %s\n", SItemName); }
                    if ((match[0] != '[') && (!feof(dat)))
                    {
                        FindFlag++;
                        if (n == 1)
                            sscanf(match, "%lf", ((double**)ItemPtr)[j + Offset] + i + Offset); //changed from [j+Offset]+i+Offset to +j+Offset+i, as ItemPtr isn't an array - 01/10: changed it back
                        else
                            sscanf(match, "%i", ((int**)ItemPtr)[j + Offset] + i + Offset);
                    }
                    else
                    {
                        i = NumItem2;
                        j = NumItem;
                    }
                }
                //Offset=Offset+(NumItem2-1); //added this line to get the correct offset in address position when incrementing j
            } //added these braces
        }
    }
    //  fprintf(stderr,"%s\n",SItemName);
    return FindFlag;
}
 
/* helper function to set icdf arrays */
void SetICDF(double* icdf, double startValue)
{
    icdf[CDF_RES] = startValue;
    for (int i = 0; i < CDF_RES; i++)
        icdf[i] = -log(1 - ((double)i) / CDF_RES);
}