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<project-file type=“source”/>

<content> #include “networkstructure.h” #include “parameters.h” #include “ode.h” #include “genrand2.h”

#include <iostream> #include <fstream>

int main(int argc, const char *argv[]) {

  Parameters params;

StringArgument ArgNet(“network”, “network data file name (output of the netgen program)”, Argument::REQUIRED);

  StringArgument ArgI0("initial-infections", "the initial infections data file name (a list of node IDs)", Argument::NOT_REQUIRED);
  LongArgument ArgSeed("seed", "the seed to initialize the random number generator", Argument::NOT_REQUIRED);	
  StringArgument ArgLog("log", "log file name", Argument::REQUIRED);
  FloatArgument ArgBetaHousehold("household-contact-rate", "the transmission rate", Argument::REQUIRED);
  FloatArgument ArgBetaExternal("external-contact-rate", "the transmission rate", Argument::REQUIRED);
  FloatArgument ArgBeta("contact-rate", "the transmission rate", Argument::REQUIRED);
  DistributionArgument ArgTinf("infectious-period", "the infectious period", Argument::REQUIRED);
  DistributionArgument ArgTlat("latent-period", "the latent period", Argument::REQUIRED);
  FloatArgument ArgQuit("quit-time", "the simulation end time", Argument::REQUIRED);
  BoolArgument ArgSIR("has-immunity", "SIR/SIS model", Argument::REQUIRED);
  IntArgument ArgRuns("runs", "the number of simulation runs", Argument::NOT_REQUIRED, 1);
  BoolArgument ArgDumpNet("dump-network", "whether to dump the contact network in the log file", Argument::NOT_REQUIRED, false);
  BoolArgument ArgCases("count-cases", "if true, count the number of new cases in each time unit, otherwise, count the number of infected individual in each time unit", Argument::NOT_REQUIRED, false);

  params.addArgument(ArgNet);
  params.addArgument(ArgI0);
  params.addArgument(ArgSeed);
  params.addArgument(ArgLog);
  params.addArgument(ArgBetaHousehold);
  params.addArgument(ArgBetaExternal);
  params.addArgument(ArgTinf);
  
  if (!params.parse(argc, argv)) {
  	params.usage(argv[0]);
  	return 1;
  }
  
  NetworkStructure net(ArgNet.value());

  // set initial infections
  std::vector<int> I0;
  int n = net.nodes();
  if (ArgI0.set()) {
      FILE *fI0 = fopen(ArgI0.value(), "r");
      if (fI0 == NULL) {
          std::cerr<<"Error: initial infections data file not readable!"<<std::endl;
          return 1;
      }
      int a;
      while (fscanf(fI0, "%d", &a) > 0)
          I0.push_back(a);
      fclose(fI0);
  }
  else
      I0.push_back(genrand2i() % n + 1);
  std::ofstream log(ArgLog.value());

  net.infect(I0);
  if (ArgDumpNet.value()) net.dumpNet(log);
  net.dumpHouseholdCompartments(log);
  net.dumpEffectiveDegrees(log);

  ODEParameters p = {
      ArgBetaHousehold.value(),
      ArgBetaExternal.value(),
      1 / ArgTinf.value()->mean(),
      net.MaxHouseholdSize,
      net.MaxExternalDegree};
  ODEResults * results = ode_simulation(p, 0, net);
  n = results->points();
  log<<"ODE:"<<std::endl;
  for (int i = 0; i < n; i++)
      log<<results->t(i)<<" : I : "<<results->It(i)<<" : "<<results->IH(i)<<std::endl;

  log.close();
  return 0;

} </content> <use name=“parameters.h”/> <use name=“ode.h”/> <use name=“networkstructure.h”/> <use name=“genrand2.h”/>