seir.cc

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// SEIR: Classical susceptible-exposed-infected-recovered model (C++)
#include "master.h"
#include "popul_proc.h"
#include "generics.h"
#include "internal.h"
 
static const int Exposed = 1;
static const int Infectious = 2;

typedef struct {
  int S;
  int E;
  int I;
  int R;
} seir_state_t;

typedef struct {
  double Beta;
  double sigma;
  double gamma;
  double psi;
  double chi;
  double omega;
  double pop;
  double S0;
  double E0;
  double I0;
  double R0;
} seir_parameters_t;
 
using seir_proc_t = popul_proc_t<seir_state_t,seir_parameters_t,6>;
using seir_genealogy_t = master_t<seir_proc_t,2>;
 
template<>
std::string seir_proc_t::yaml (std::string tab) const {
  std::string t = tab + "  ";
  std::string p = tab + "parameter:\n"
    + YAML_PARAM(Beta)
    + YAML_PARAM(sigma)
    + YAML_PARAM(gamma)
    + YAML_PARAM(psi)
    + YAML_PARAM(chi)
    + YAML_PARAM(omega)
    + YAML_PARAM(pop)
    + YAML_PARAM(S0)
    + YAML_PARAM(E0)
    + YAML_PARAM(I0)
    + YAML_PARAM(R0);
  std::string s = tab + "state:\n"
    + YAML_STATE(S)
    + YAML_STATE(E)
    + YAML_STATE(I)
    + YAML_STATE(R);
  return p+s;
}
 
template<>
void seir_proc_t::update_params (double *p, int n) {
  int m = 0;
  PARAM_SET(Beta);
  PARAM_SET(sigma);
  PARAM_SET(gamma);
  PARAM_SET(psi);
  PARAM_SET(chi);
  PARAM_SET(omega);
  if (m != n) err("wrong number of parameters!");
}
 
template<>
void seir_proc_t::update_IVPs (double *p, int n) {
  int m = 0;
  PARAM_SET(pop);
  PARAM_SET(S0);
  PARAM_SET(E0);
  PARAM_SET(I0);
  PARAM_SET(R0);
  if (m != n) err("wrong number of initial-value parameters!");
}
 
template<>
double seir_proc_t::event_rates (double *rate, int n) const {
  int m = 0;
  double total = 0;
  RATE_CALC(params.Beta * state.S * state.I / params.pop);
  RATE_CALC(params.sigma * state.E);
  RATE_CALC(params.gamma * state.I);
  RATE_CALC(params.chi * state.I);
  RATE_CALC(params.psi * state.I);
  RATE_CALC(params.omega * state.R);
  if (m != n) err("wrong number of events!");
  return total;
}
 
template<>
void seir_genealogy_t::rinit (void) {
  double f = params.pop/(params.S0+params.E0+params.I0+params.R0);
  state.S = nearbyint(f*params.S0);
  state.E = nearbyint(f*params.E0);
  state.I = nearbyint(f*params.I0);
  state.R = nearbyint(f*params.R0);
  graft(Exposed,state.E);
  graft(Infectious,state.I);
}
 
template<>
void seir_genealogy_t::jump (int event) {
  switch (event) {
  case 0:
    state.S -= 1; state.E += 1; birth(Infectious,Exposed);
    break;
  case 1:
    state.E -= 1; state.I += 1; migrate(Exposed,Infectious);
    break;
  case 2:
    state.I -= 1; state.R += 1; death(Infectious);
    break;
  case 3:
    state.I -= 1; sample_death(Infectious);
    break;
  case 4:
    sample(Infectious);
    break;
  case 5:
    state.R -= 1; state.S += 1;
    break;
  default:                      // #nocov
    assert(0);                  // #nocov
    break;                      // #nocov
  }
}
 
GENERICS(SEIR,seir_genealogy_t)