twospecies_pomp.c File Reference

#include "pomplink.h"
#include "internal.h"

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Macros
#define	host1   0
#define	host2   1
#define	Beta11   (__p[__parindex[0]])
#define	Beta12   (__p[__parindex[1]])
#define	Beta21   (__p[__parindex[2]])
#define	Beta22   (__p[__parindex[3]])
#define	gamma1   (__p[__parindex[4]])
#define	gamma2   (__p[__parindex[5]])
#define	psi1   (__p[__parindex[6]])
#define	psi2   (__p[__parindex[7]])
#define	omega1   (__p[__parindex[8]])
#define	omega2   (__p[__parindex[9]])
#define	b1   (__p[__parindex[10]])
#define	b2   (__p[__parindex[11]])
#define	d1   (__p[__parindex[12]])
#define	d2   (__p[__parindex[13]])
#define	C1   (__p[__parindex[14]])
#define	C2   (__p[__parindex[15]])
#define	S1_0   (__p[__parindex[16]])
#define	S2_0   (__p[__parindex[17]])
#define	I1_0   (__p[__parindex[18]])
#define	I2_0   (__p[__parindex[19]])
#define	R1_0   (__p[__parindex[20]])
#define	R2_0   (__p[__parindex[21]])
#define	S1   (__x[__stateindex[0]])
#define	S2   (__x[__stateindex[1]])
#define	I1   (__x[__stateindex[2]])
#define	I2   (__x[__stateindex[3]])
#define	R1   (__x[__stateindex[4]])
#define	R2   (__x[__stateindex[5]])
#define	N1   (__x[__stateindex[6]])
#define	N2   (__x[__stateindex[7]])
#define	ll   (__x[__stateindex[8]])
#define	node   (__x[__stateindex[9]])
#define	ell1   (__x[__stateindex[10]])
#define	ell2   (__x[__stateindex[11]])
#define	COLOR   (__x[__stateindex[12]])
#define	EVENT_RATES
#define	lik   (__lik[0])

Functions
static int	random_choice (double n)
static void	change_color (double *color, int nsample, int n, int from, int to)
static int	check_color (double *color, int nsample, double size1, double size2)
static double	event_rates (double *__x, const double *__p, double t, const int *__stateindex, const int *__parindex, const int *__covindex, const double *__covars, double *rate, double *logpi, double *penalty)
void	twospecies_rinit (double *__x, const double *__p, double t0, const int *__stateindex, const int *__parindex, const int *__covindex, const double *__covars)
void	twospecies_gill (double *__x, const double *__p, const int *__stateindex, const int *__parindex, const int *__covindex, const double *__covars, double t, double dt)
void	twospecies_dmeas (double *__lik, const double *__y, const double *__x, const double *__p, int give_log, const int *__obsindex, const int *__stateindex, const int *__parindex, const int *__covindex, const double *__covars, double t)
	Measurement model likelihood (dmeasure).

Variables
static const int	nrate = 18

Macro Definition Documentation

b1

#define b1   (__p[__parindex[10]])

Definition at line 51 of file twospecies_pomp.c.

b2

#define b2   (__p[__parindex[11]])

Definition at line 52 of file twospecies_pomp.c.

Beta11

#define Beta11   (__p[__parindex[0]])

Definition at line 41 of file twospecies_pomp.c.

Beta12

#define Beta12   (__p[__parindex[1]])

Definition at line 42 of file twospecies_pomp.c.

Beta21

#define Beta21   (__p[__parindex[2]])

Definition at line 43 of file twospecies_pomp.c.

Beta22

#define Beta22   (__p[__parindex[3]])

Definition at line 44 of file twospecies_pomp.c.

C1

#define C1   (__p[__parindex[14]])

Definition at line 55 of file twospecies_pomp.c.

C2

#define C2   (__p[__parindex[15]])

Definition at line 56 of file twospecies_pomp.c.

COLOR

#define COLOR   (__x[__stateindex[12]])

Definition at line 75 of file twospecies_pomp.c.

d1

#define d1   (__p[__parindex[12]])

Definition at line 53 of file twospecies_pomp.c.

d2

#define d2   (__p[__parindex[13]])

Definition at line 54 of file twospecies_pomp.c.

ell1

#define ell1   (__x[__stateindex[10]])

Definition at line 73 of file twospecies_pomp.c.

ell2

#define ell2   (__x[__stateindex[11]])

Definition at line 74 of file twospecies_pomp.c.

EVENT_RATES

#define EVENT_RATES

Value:

  event_rates(__x,__p,t,                                \
              __stateindex,__parindex,__covindex,       \
              __covars,rate,logpi,&penalty)             \

Definition at line 77 of file twospecies_pomp.c.

#define EVENT_RATES                                     \
  event_rates(__x,__p,t,                                \
              __stateindex,__parindex,__covindex,       \
              __covars,rate,logpi,&penalty)             \
 

gamma1

#define gamma1   (__p[__parindex[4]])

Definition at line 45 of file twospecies_pomp.c.

gamma2

#define gamma2   (__p[__parindex[5]])

Definition at line 46 of file twospecies_pomp.c.

host1

#define host1   0

Definition at line 5 of file twospecies_pomp.c.

host2

#define host2   1

Definition at line 6 of file twospecies_pomp.c.

I1

#define I1   (__x[__stateindex[2]])

Definition at line 65 of file twospecies_pomp.c.

I1_0

#define I1_0   (__p[__parindex[18]])

Definition at line 59 of file twospecies_pomp.c.

I2

#define I2   (__x[__stateindex[3]])

Definition at line 66 of file twospecies_pomp.c.

I2_0

#define I2_0   (__p[__parindex[19]])

Definition at line 60 of file twospecies_pomp.c.

lik

#define lik   (__lik[0])

Definition at line 634 of file twospecies_pomp.c.

ll

#define ll   (__x[__stateindex[8]])

Definition at line 71 of file twospecies_pomp.c.

N1

#define N1   (__x[__stateindex[6]])

Definition at line 69 of file twospecies_pomp.c.

N2

#define N2   (__x[__stateindex[7]])

Definition at line 70 of file twospecies_pomp.c.

node

#define node   (__x[__stateindex[9]])

Definition at line 72 of file twospecies_pomp.c.

omega1

#define omega1   (__p[__parindex[8]])

Definition at line 49 of file twospecies_pomp.c.

omega2

#define omega2   (__p[__parindex[9]])

Definition at line 50 of file twospecies_pomp.c.

psi1

#define psi1   (__p[__parindex[6]])

Definition at line 47 of file twospecies_pomp.c.

psi2

#define psi2   (__p[__parindex[7]])

Definition at line 48 of file twospecies_pomp.c.

R1

#define R1   (__x[__stateindex[4]])

Definition at line 67 of file twospecies_pomp.c.

R1_0

#define R1_0   (__p[__parindex[20]])

Definition at line 61 of file twospecies_pomp.c.

R2

#define R2   (__x[__stateindex[5]])

Definition at line 68 of file twospecies_pomp.c.

R2_0

#define R2_0   (__p[__parindex[21]])

Definition at line 62 of file twospecies_pomp.c.

S1

#define S1   (__x[__stateindex[0]])

Definition at line 63 of file twospecies_pomp.c.

S1_0

#define S1_0   (__p[__parindex[16]])

Definition at line 57 of file twospecies_pomp.c.

S2

#define S2   (__x[__stateindex[1]])

Definition at line 64 of file twospecies_pomp.c.

S2_0

#define S2_0   (__p[__parindex[17]])

Definition at line 58 of file twospecies_pomp.c.

Function Documentation

change_color()

static void change_color ( double * color, int nsample, int n, int from, int to )

static

Definition at line 12 of file twospecies_pomp.c.

                                                   {
  int i = -1;
  while (n >= 0 && i < nsample) {
    i++;
    if (!ISNA(color[i]) && nearbyint(color[i]) == from) n--;
  }
  assert(i < nsample);
  assert(n == -1);
  assert(nearbyint(color[i]) == from);
  color[i] = to;
}

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check_color()

static int check_color ( double * color, int nsample, double size1, double size2 )

static

Definition at line 26 of file twospecies_pomp.c.

                                                    {
  int n1 = 0, n2 = 0;
  int s1 = (int) nearbyint(size1);
  int s2 = (int) nearbyint(size2);
  for (int i = 0; i < nsample; i++) {
    if (!ISNA(color[i])) {
      if (nearbyint(color[i]) == host1) n1++;
      if (nearbyint(color[i]) == host2) n2++;
    }
  }
  return (n1==s1) && (n2==s2);
}

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event_rates()

static double event_rates ( double * __x, const double * __p, double t, const int * __stateindex, const int * __parindex, const int * __covindex, const double * __covars, double * rate, double * logpi, double * penalty )

static

Definition at line 84 of file twospecies_pomp.c.

   {
  double event_rate = 0;
  double alpha, pi, disc;
  *penalty = 0;
  // 0: Trans_11, s = (0,0),(1,0)
  assert(S1>=0 && I1>=ell1 && ell1>=0);
  alpha = (N1 > 0) ? Beta11*S1*I1/N1 : 0;
  disc = (I1 > 0) ? ell1*(ell1-1)/I1/(I1+1) : 1;
  *penalty += alpha*disc;
  event_rate += (*rate = alpha*(1-disc)); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 1: Trans_22, s = (0,0),(0,1)
  assert(S2>=0 && I2>=ell2 && ell2>=0);
  alpha = (N2 > 0) ? Beta22*S2*I2/N2 : 0;
  disc = (I2 > 0) ? ell2*(ell2-1)/I2/(I2+1) : 1;
  *penalty += alpha*disc;
  event_rate += (*rate = alpha*(1-disc)); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 2: Trans_21, s = (0,0),(1,0)
  // s = (0,0): pi = (I1-ell1)/I1, m = 1,
  // s = (1,0): pi = 1/(2*I1), m = ell1
  // total pi = (I1-0.5*ell1)/I1
  assert(S2>=0 && I1>=ell1 && ell1>=0);
  alpha = (N1 > 0) ? Beta21*S2*I1/N1 : 0;
  pi = (I1 > 0) ? (I1-0.5*ell1)/I1 : 1;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi); logpi++;
  assert(R_FINITE(event_rate));
  // 3: Trans_21, s = (0,1)
  // s = (0,1): pi = 1/(2*I1), m = ell1
  pi = (I1 > 0) ? 1-pi : 1;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi)-log(ell1); logpi++;
  assert(R_FINITE(event_rate));
  // 4: Trans_12, s = (0,0),(0,1)
  assert(S1>=0 && I2>=ell2 && ell2>=0);
  alpha = (N2 > 0) ? Beta12*S1*I2/N2 : 0;
  pi = (I2 > 0) ? (I2-ell2*0.5)/I2 : 1;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi); logpi++;
  assert(R_FINITE(event_rate));
  // 5: Trans_12, s = (1,0)
  pi = (I2 > 0) ? 1-pi : 0;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi)-log(ell2); logpi++;
  assert(R_FINITE(event_rate));
  // 6: Recov_1
  assert(I1>=0 && ell1>=0);
  alpha = gamma1*I1;
  if (I1 > ell1) {
    event_rate += (*rate = alpha); rate++;
  } else {
    *rate = 0; rate++;
    *penalty += alpha;
  }
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 7: Recov_2
  assert(I2>=0 && ell2>=0);
  alpha = gamma2*I2;
  if (I2 > ell2) {
    event_rate += (*rate = alpha); rate++;
  } else {
    *rate = 0; rate++;
    *penalty += alpha;
  }
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 8: Wane_1
  assert(R1>=0);
  alpha = omega1*R1;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 9: Wane_2
  assert(R2>=0);
  alpha = omega2*R2;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 10: Birth_1
  assert(N1>=0);
  alpha = b1*N1;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 11: Birth_2
  assert(N2>=0);
  alpha = b2*N2;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 12: Death_S1
  assert(S1>=0);
  alpha = d1*S1;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 13: Death_I1
  assert(I1>=0);
  alpha = d1*I1;
  if (I1 > ell1) {
    event_rate += (*rate = alpha); rate++;
  } else {
    *rate = 0; rate++;
    *penalty += alpha;
  }
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 14: Death_R1
  assert(R1>=0);
  alpha = d1*R1;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 15: Death_S2
  assert(S2>=0);
  alpha = d2*S2;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 16: Death_I2
  assert(I2>=0);
  alpha = d2*I2;
  if (I2 > ell2) {
    event_rate += (*rate = alpha); rate++;
  } else {
    *rate = 0; rate++;
    *penalty += alpha;
  }
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // 17: Death_R2
  assert(R2>=0);
  alpha = d2*R2;
  event_rate += (*rate = alpha); rate++;
  *logpi = 0; logpi++;
  assert(R_FINITE(event_rate));
  // Sample_1 (Q = 0) // NB: (1-C1)*psi1+C1*psi1 = psi1
  *penalty += psi1*I1;
  // Sample_2 (Q = 0) // NB: (1-C2)*psi2+C2*psi2 = psi2
  *penalty += psi2*I2;
  return event_rate;
}

random_choice()

static int random_choice ( double n )

inlinestatic

Definition at line 8 of file twospecies_pomp.c.

                                           {
  return floor(R_unif_index(n));
}

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twospecies_dmeas()

void twospecies_dmeas	(	double *	__lik,
		const double *	__y,
		const double *	__x,
		const double *	__p,
		int	give_log,
		const int *	__obsindex,
		const int *	__stateindex,
		const int *	__parindex,
		const int *	__covindex,
		const double *	__covars,
		double	t )

Measurement model likelihood (dmeasure).

Definition at line 637 of file twospecies_pomp.c.

   {
  assert(!ISNAN(ll));
  lik = (give_log) ? ll : exp(ll);
}

twospecies_gill()

void twospecies_gill	(	double *	__x,
		const double *	__p,
		const int *	__stateindex,
		const int *	__parindex,
		const int *	__covindex,
		const double *	__covars,
		double	t,
		double	dt )

Simulator for the latent-state process (rprocess).

This is the Gillespie algorithm applied to the solution of the filter equation for the TwoSpecies model. It advances the state from time t to time t+dt.

A tricky aspect of this function is that it must return a "valid" state even when the state is incompatible with the genealogy. In such a case, we set the log likelihood (ll) to R_NegInf, but the state must remain valid. Hence insertion of extra infectives, etc.

FIXME: At the moment, the following codes exclude the possibility of importation of infection.

Definition at line 290 of file twospecies_pomp.c.

  {
  double tstep = 0.0, tmax = t + dt;
  double *color = &COLOR;
  const int nsample = *get_userdata_int("nsample");
  const int *nodetype = get_userdata_int("nodetype");
  const int *nodedeme = get_userdata_int("deme");
  const int *lineage = get_userdata_int("lineage");
  const int *sat = get_userdata_int("saturation");
  const int *index = get_userdata_int("index");
  const int *child = get_userdata_int("child");
 
  int parent = (int) nearbyint(node);
 
#ifndef NDEBUG
  int nnode = *get_userdata_int("nnode");
  assert(parent>=0);
  assert(parent<=nnode);
#endif
 
  int parlin = lineage[parent];
  int parcol = color[parlin];
  int deme = nodedeme[parent];
  assert(parlin >= 0 && parlin < nsample);
  assert(nearbyint(N1)==nearbyint(S1+I1+R1));
  assert(nearbyint(N2)==nearbyint(S2+I2+R2));
  assert(check_color(color,nsample,ell1,ell2));
 
  ll = 0;
 
  // singular portion of filter equation
  switch (nodetype[parent]) {
  default:                      // non-genealogical event
    break;
  case 0:                       // root
    // color lineages by sampling without replacement
    assert(sat[parent]==1);
    int c = child[index[parent]];
    assert(parlin==lineage[c]);
    if (I1-ell1+I2-ell2 > 0) {
      double x = (I1-ell1)/(I1-ell1 + I2-ell2);
      if (unif_rand() < x) {    // lineage is put into I1 deme
        color[lineage[c]] = host1;
        ell1 += 1;
        ll -= log(x);
      } else {                  // lineage is put into I2 deme
        color[lineage[c]] = host2;
        ell2 += 1;
        ll -= log(1-x);
      }
    } else {                // more roots than infectives
      ll += R_NegInf;       // this is incompatible with the genealogy
      // the following keeps the state valid
      if (unif_rand() < 0.5) {  // lineage is put into I1 deme
        color[lineage[c]] = host1;
        ell1 += 1; I1 += 1; N1 += 1;
      } else {                  // lineage is put into I2 deme
        color[lineage[c]] = host2;
        ell2 += 1; I2 += 1; N2 += 1;
      }
    }
    assert(nearbyint(N1)==nearbyint(S1+I1+R1));
    assert(nearbyint(N2)==nearbyint(S2+I2+R2));
    assert(check_color(color,nsample,ell1,ell2));
    break;
  case 1:                       // sample
    if (parcol != deme) { // parent color does not match the observed deme
      ll += R_NegInf;
    }
    if (sat[parent] == 0) {     // s=(0,0)
      if (parcol == host1) {
        ell1 -= 1;
        if (C1 < 1 && unif_rand() > C1) {
          ll += log(psi1*(I1-ell1));
        } else {
          ll += log(psi1*I1);
          I1 -= 1; N1 -= 1;
        }
      } else if (parcol == host2) {
        ell2 -= 1;
        if (C2 < 1 && unif_rand() > C2) {
          ll += log(psi2*(I2-ell2));
        } else {
          ll += log(psi2*I2);
          I2 -= 1; N2 -= 1;
        }
      } else {
        assert(0);              // #nocov
        ll += R_NegInf;         // #nocov
      }
    } else if (sat[parent] == 1) {
      int c = child[index[parent]];
      color[lineage[c]] = parcol;
      if (parcol==host1) {
        ll += log(psi1*(1-C1)); // s=(1,0)
      } else if (parcol==host2) {
        ll += log(psi2*(1-C2)); // s=(0,1)
      } else {
        assert(0);              // #nocov
        ll += R_NegInf;         // #nocov
      }
    } else {
      assert(0);                // #nocov
      ll += R_NegInf;           // #nocov
    }
    color[parlin] = R_NaReal;
    assert(nearbyint(N1)==nearbyint(S1+I1+R1));
    assert(nearbyint(N2)==nearbyint(S2+I2+R2));
    assert(check_color(color,nsample,ell1,ell2));
    break;
  case 2:                       // branch point
    assert(sat[parent]==2);
    if (parcol == host1) {      // parent is in I1
      assert(S1>=0 && S2 >=0 && I1>=ell1 && ell1>=0);
      double lambda11 = Beta11*S1*I1/N1;
      double lambda21 = Beta21*S2*I1/N1;
      double lambda = lambda11+lambda21;
      double x = (lambda > 0) ? lambda11/lambda : 0;
      int c1 = child[index[parent]];
      int c2 = child[index[parent]+1];
      assert(c1 != c2);
      assert(lineage[c1] != lineage[c2]);
      assert(lineage[c1] != parlin || lineage[c2] != parlin);
      assert(lineage[c1] == parlin || lineage[c2] == parlin);
      if (unif_rand() < x) {    // s = (2,0)
        color[lineage[c1]] = host1;
        color[lineage[c2]] = host1;
        if (S1 > 0) {
          S1 -= 1; I1 += 1; ell1 += 1;
          ll += log(lambda)-log(I1*(I1-1)/2);
        } else {
          // the genealogy is incompatible with the state.
          // nevertheless, the state remains valid.
          I1 += 1; N1 += 1; ell1 += 1;
          ll += R_NegInf;
        }
      } else {                  // s = (1,1)
        if (unif_rand() < 0.5) {
          color[lineage[c1]] = host1;
          color[lineage[c2]] = host2;
        } else {
          color[lineage[c1]] = host2;
          color[lineage[c2]] = host1;
        }
        ll -= log(0.5);
        if (S2 > 0) {
          S2 -= 1; I2 += 1; ell2 += 1;
          ll += log(lambda)-log(I1*I2);
        } else {
          // the genealogy is incompatible with the state.
          // nevertheless, the state remains valid.
          I2 += 1; N2 += 1; ell2 += 1;
          ll += R_NegInf;
        }
      }
    } else if (parcol == host2) { // parent is in I2
      assert(S1>=0 && S2 >=0 && I2>=ell2);
      double lambda12 = Beta12*S1*I2/N2;
      double lambda22 = Beta22*S2*I2/N2;
      double lambda = lambda12+lambda22;
      double x = (lambda > 0) ? lambda22/lambda : 0;
      int c1 = child[index[parent]];
      int c2 = child[index[parent]+1];
      assert(c1 != c2);
      assert(lineage[c1] != lineage[c2]);
      assert(lineage[c1] != parlin || lineage[c2] != parlin);
      assert(lineage[c1] == parlin || lineage[c2] == parlin);
      if (unif_rand() < x) { // s = (0,2)
        color[lineage[c1]] = host2;
        color[lineage[c2]] = host2;
        if (S2 > 0) {
          S2 -= 1; I2 += 1; ell2 += 1;
          ll += log(lambda)-log(I2*(I2-1)/2);
        } else {
          // the genealogy is incompatible with the state.
          // nevertheless, the state remains valid.
          I2 += 1; N2 += 1; ell2 += 1;
          ll += R_NegInf;
        }
      } else {                  // s = (1,1)
        if (unif_rand() < 0.5) {
          color[lineage[c1]] = host1;
          color[lineage[c2]] = host2;
        } else {
          color[lineage[c1]] = host2;
          color[lineage[c2]] = host1;
        }
        ll -= log(0.5);
        if (S1 > 0) {
          S1 -= 1; I1 += 1; ell1 += 1;
          ll += log(lambda)-log(I1*I2);
        } else {
          // the genealogy is incompatible with the state.
          // nevertheless, the state remains valid.
          I1 += 1; N1 += 1; ell1 += 1;
          ll += R_NegInf;
        }
      }
    } else {
      assert(0);                // #nocov
      ll += R_NegInf;           // #nocov
    }
    assert(nearbyint(N1)==nearbyint(S1+I1+R1));
    assert(nearbyint(N2)==nearbyint(S2+I2+R2));
    assert(check_color(color,nsample,ell1,ell2));
    break;
  }
 
  // continuous portion of filter equation:
  // take Gillespie steps to the end of the interval.
  if (tmax > t) {
 
    double rate[nrate], logpi[nrate];
    int event;
    double event_rate = 0;
    double penalty = 0;
 
    event_rate = EVENT_RATES;
    tstep = exp_rand()/event_rate;
 
    while (t + tstep < tmax) {
      event = rcateg(event_rate,rate,nrate);
      assert(event>=0 && event<nrate);
      ll -= penalty*tstep + logpi[event];
      switch (event) {
      case 0:                   // 0: Trans_11, s = (0,0),(1,0)
        assert(S1>=1 && I1>=0);
        S1 -= 1; I1 += 1;
        break;
      case 1:                   // 1: Trans_22, s = (0,0),(0,1)
        assert(S2>=1 && I2>=0);
        S2 -= 1; I2 += 1;
        break;
      case 2:                   // 2: Trans_21, s = (0,0),(1,0)
        assert(S2>=1 && I1>=0);
        S2 -= 1; I2 += 1;
        ll += log(1-ell2/I2);
        assert(!ISNAN(ll));
        break;
      case 3:                   // 3: Trans_21, s = (0,1)
        assert(S2>=1 && I1>=0);
        S2 -= 1; I2 += 1;
        change_color(color,nsample,random_choice(ell1),host1,host2);
        ell1 -= 1; ell2 += 1;
        ll += log(1-ell1/I1)-log(I2);
        assert(check_color(color,nsample,ell1,ell2));
        assert(!ISNAN(ll));
        break;
      case 4:                   // 4: Trans_12, s = (0,0),(0,1)
        assert(S1>=1 && I2>=0);
        S1 -= 1; I1 += 1;
        ll += log(1-ell1/I1);
        assert(!ISNAN(ll));
        break;
      case 5:                   // 5: Trans_12, s = (1,0)
        assert(S1>=1 && I2>=0);
        S1 -= 1; I1 += 1;
        change_color(color,nsample,random_choice(ell2),host2,host1);
        ell2 -= 1; ell1 += 1;
        ll += log(1-ell2/I2)-log(I1);
        assert(check_color(color,nsample,ell1,ell2));
        assert(!ISNAN(ll));
        break;
      case 6:                   // 6: Recov_1
        assert(I1>=1);
        I1 -= 1; R1 += 1;
        break;
      case 7:                   // 7: Recov_2
        assert(I2>=1);
        I2 -= 1; R2 += 1;
        break;
      case 8:                   // 8: Wane_1
        assert(R1>=1);
        R1 -= 1; S1 += 1;
        break;
      case 9:                   // 9: Wane_2
        assert(R2>=1);
        R2 -= 1; S2 += 1;
        break;
      case 10:                  // 10: Birth_1
        assert(N1>=1);
        S1 += 1; N1 += 1;
        break;
      case 11:                  // 11: Birth_2
        assert(N2>=1);
        S2 += 1; N2 += 1;
        break;
      case 12:                  // 12: Death_S1
        assert(S1>=1 && N1>=1);
        S1 -= 1; N1 -= 1;
        break;
      case 13:                  // 13: Death_I1
        assert(I1>=1 && N1>=1);
        I1 -= 1; N1 -= 1;
        break;
      case 14:                  // 14: Death_R1
        assert(R1>=1 && N1>=1);
        R1 -= 1; N1 -= 1;
        break;
      case 15:                  // 15: Death_S2
        assert(S2>=1 && N2>=1);
        S2 -= 1; N2 -= 1;
        break;
      case 16:                  // 16: Death_I2
        assert(I2>=1 && N2>=1);
        I2 -= 1; N2 -= 1;
        break;
      case 17:                  // 17: Death_R2
        assert(R2>=1 && N2>=1);
        R2 -= 1; N2 -= 1;
        break;
      default:                  // #nocov
        assert(0);              // #nocov
        ll += R_NegInf;         // #nocov
        break;                  // #nocov
      }
 
      ell1 = nearbyint(ell1);
      ell2 = nearbyint(ell2);
 
      assert(nearbyint(N1)==nearbyint(S1+I1+R1));
      assert(nearbyint(N2)==nearbyint(S2+I2+R2));
      assert(check_color(color,nsample,ell1,ell2));
 
      t += tstep;
      event_rate = EVENT_RATES;
      tstep = exp_rand()/event_rate;
 
    }
    tstep = tmax - t;
    ll -= penalty*tstep;
  }
  node += 1;
}

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twospecies_rinit()

void twospecies_rinit	(	double *	__x,
		const double *	__p,
		double	t0,
		const int *	__stateindex,
		const int *	__parindex,
		const int *	__covindex,
		const double *	__covars )

Latent-state initializer (rinit component).

The state variables include S, E, I, R plus 'ellE' and 'ellI' (numbers of E- and I-deme lineages), the accumulated weight ('ll'), the current node number ('node'), and the coloring of each lineage ('COLOR').

Definition at line 249 of file twospecies_pomp.c.

  {
  double adj;
  N1 = S1_0+I1_0+R1_0;
  N2 = S2_0+I2_0+R2_0;
  adj = N1/(S1_0+I1_0+R1_0);
  S1 = nearbyint(S1_0*adj);
  I1 = nearbyint(I1_0*adj);
  R1 = N1-S1-I1;
  adj = N2/(S2_0+I2_0+R2_0);
  S2 = nearbyint(S2_0*adj);
  I2 = nearbyint(I2_0*adj);
  R2 = N2-S2-I2;
  ell1 = 0;
  ell2 = 0;
  ll = 0;
  node = 0;
}

Variable Documentation

nrate

const int nrate = 18

static

Definition at line 4 of file twospecies_pomp.c.