si2r_pomp.c File Reference

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

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Macros
#define	Low   1
#define	High   2
#define	Beta   (__p[__parindex[0]])
#define	kappa   (__p[__parindex[1]])
#define	gamma   (__p[__parindex[2]])
#define	omega   (__p[__parindex[3]])
#define	chi   (__p[__parindex[4]])
#define	etaL   (__p[__parindex[5]])
#define	etaH   (__p[__parindex[6]])
#define	POP   (__p[__parindex[7]])
#define	S0   (__p[__parindex[8]])
#define	IL0   (__p[__parindex[9]])
#define	IH0   (__p[__parindex[10]])
#define	R0   (__p[__parindex[11]])
#define	S   (__x[__stateindex[0]])
#define	IL   (__x[__stateindex[1]])
#define	IH   (__x[__stateindex[2]])
#define	R   (__x[__stateindex[3]])
#define	ll   (__x[__stateindex[4]])
#define	node   (__x[__stateindex[5]])
#define	ellL   (__x[__stateindex[6]])
#define	ellH   (__x[__stateindex[7]])
#define	COLOR   (__x[__stateindex[8]])
#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 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 *decay)
void	si2rs_rinit (double *__x, const double *__p, double t0, const int *__stateindex, const int *__parindex, const int *__covindex, const double *__covars)
void	si2rs_gill (double *__x, const double *__p, const int *__stateindex, const int *__parindex, const int *__covindex, const double *__covars, double t, double dt)
void	si2rs_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 = 10

Macro Definition Documentation

Beta

#define Beta   (__p[__parindex[0]])

Definition at line 26 of file si2r_pomp.c.

chi

#define chi   (__p[__parindex[4]])

Definition at line 30 of file si2r_pomp.c.

COLOR

#define COLOR   (__x[__stateindex[8]])

Definition at line 46 of file si2r_pomp.c.

ellH

#define ellH   (__x[__stateindex[7]])

Definition at line 45 of file si2r_pomp.c.

ellL

#define ellL   (__x[__stateindex[6]])

Definition at line 44 of file si2r_pomp.c.

etaH

#define etaH   (__p[__parindex[6]])

Definition at line 32 of file si2r_pomp.c.

etaL

#define etaL   (__p[__parindex[5]])

Definition at line 31 of file si2r_pomp.c.

EVENT_RATES

#define EVENT_RATES

Value:

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

Definition at line 48 of file si2r_pomp.c.

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

gamma

#define gamma   (__p[__parindex[2]])

Definition at line 28 of file si2r_pomp.c.

High

#define High   2

Definition at line 5 of file si2r_pomp.c.

IH

#define IH   (__x[__stateindex[2]])

Definition at line 40 of file si2r_pomp.c.

IH0

#define IH0   (__p[__parindex[10]])

Definition at line 36 of file si2r_pomp.c.

IL

#define IL   (__x[__stateindex[1]])

Definition at line 39 of file si2r_pomp.c.

IL0

#define IL0   (__p[__parindex[9]])

Definition at line 35 of file si2r_pomp.c.

kappa

#define kappa   (__p[__parindex[1]])

Definition at line 27 of file si2r_pomp.c.

lik

#define lik   (__lik[0])

Definition at line 397 of file si2r_pomp.c.

ll

#define ll   (__x[__stateindex[4]])

Definition at line 42 of file si2r_pomp.c.

Low

#define Low   1

Definition at line 4 of file si2r_pomp.c.

node

#define node   (__x[__stateindex[5]])

Definition at line 43 of file si2r_pomp.c.

omega

#define omega   (__p[__parindex[3]])

Definition at line 29 of file si2r_pomp.c.

POP

#define POP   (__p[__parindex[7]])

Definition at line 33 of file si2r_pomp.c.

R

#define R   (__x[__stateindex[3]])

Definition at line 41 of file si2r_pomp.c.

R0

#define R0   (__p[__parindex[11]])

Definition at line 37 of file si2r_pomp.c.

S

#define S   (__x[__stateindex[0]])

Definition at line 38 of file si2r_pomp.c.

S0

#define S0   (__p[__parindex[8]])

Definition at line 34 of file si2r_pomp.c.

Function Documentation

change_color()

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

static

Definition at line 13 of file si2r_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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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 * decay )

static

Definition at line 53 of file si2r_pomp.c.

   {
  double event_rate = 0;
  double alpha, pi;
  *decay = 0;
  assert(R_FINITE(event_rate));
  // 0: TL, s=(0,0) or s=(1,0)
  assert(S>=0 && IL>=0);
  alpha = (POP > 0) ? Beta*S*IL/POP : 0;
  assert(IL >= ellL);
  pi = 1;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi); logpi++;
  assert(R_FINITE(event_rate));
  // 1: TH, s=(0,0)
  assert(S>=0 && IH>=0);
  alpha = (POP > 0) ? kappa*Beta*S*IH/POP : 0;
  assert(IH >= ellH);
  pi = (IH > 0) ? 1-0.5*ellH/IH : 1;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi); logpi++;
  assert(R_FINITE(event_rate));
  // 2: TH, s=(1,0)
  pi = 1-pi;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi/ellH); logpi++;
  assert(R_FINITE(event_rate));
  // 3: L, s=(0,0)
  assert(IL>=0);
  alpha = etaL*IL;
  assert(IL >= ellL);
  pi = (IL > 0) ? 1-ellL/IL : 1;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi); logpi++;
  assert(R_FINITE(event_rate));
  // 4: L, s=(0,1)
  pi = 1-pi;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi/ellL); logpi++;
  assert(R_FINITE(event_rate));
  // 5: H, s=(0,0)
  assert(IH>=0);
  alpha = etaH*IH;
  assert(IH >= ellH);
  pi = (IH > 0) ? 1-ellH/IH : 1;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi); logpi++;
  assert(R_FINITE(event_rate));
  // 6: H, s=(1,0)
  pi = 1-pi;
  event_rate += (*rate = alpha*pi); rate++;
  *logpi = log(pi/ellH); logpi++;
  assert(R_FINITE(event_rate));
  // 7: RL
  assert(IL>=0);
  alpha = gamma*IL;
  if (IL > ellL) {
    event_rate += (*rate = alpha); rate++;
    *logpi = 0; logpi++;
  } else {
    *rate = 0; rate++;
    *logpi = 0; logpi++;
    *decay += alpha;
  }
  assert(R_FINITE(event_rate));
  // 8: RH
  assert(IH>=0);
  alpha = gamma*IH;
  if (IH > ellH) {
    event_rate += (*rate = alpha); rate++;
    *logpi = 0; logpi++;
  } else {
    *rate = 0; rate++;
    *logpi = 0; logpi++;
    *decay += alpha;
  }
  assert(R_FINITE(event_rate));
  // 9: W
  event_rate += (*rate = omega*R); rate++;
  *logpi = 0; logpi++;
  // sampling
  *decay += chi*(IL+IH);
  assert(R_FINITE(event_rate));
  return event_rate;
}

random_choice()

static int random_choice ( double n )

inlinestatic

Definition at line 9 of file si2r_pomp.c.

                                           {
  return floor(R_unif_index(n));
}

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si2rs_dmeas()

void si2rs_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 400 of file si2r_pomp.c.

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

si2rs_gill()

void si2rs_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 SI2RS process.

Definition at line 181 of file si2r_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 *lineage = get_userdata_int("lineage");
  const int *index = get_userdata_int("index");
  const int *child = get_userdata_int("child");
 
  int parent = (int) nearbyint(node);
 
#ifndef NDEBUG
  const int *sat = get_userdata_int("saturation");
  int nnode = *get_userdata_int("nnode");
  assert(parent>=0);
  assert(parent<=nnode);
#endif
 
  int parlin = lineage[parent];
  int parcol = color[parlin];
  assert(parlin >= 0 && parlin < nsample);
 
  ll = 0;
 
  // singular portion of filter equation
  switch (nodetype[parent]) {
  default:                      // non-genealogical event #nocov
    break;                      // #nocov
  case 0:                       // root
    // color lineages by sampling without replacement
    assert(sat[parent]==1);
    int c = child[index[parent]];
    assert(lineage[parent]==lineage[c]);
    if (IL-ellL + IH-ellH > 0) {
      double x = (IL-ellL)/(IL-ellL + IH-ellH);
      if (unif_rand() < x) {      // lineage is put into Low deme
        color[lineage[c]] = Low;
        ellL += 1;
        ll -= log(x);
      } else {                    // lineage is put into High deme
        color[lineage[c]] = High;
        ellH += 1;
        ll -= log(1-x);
      }
      assert(!ISNAN(ll));
    } else {                // more roots than infectives
      ll += R_NegInf;       // this is incompatible with the genealogy
      // the following keeps the state valid
      color[lineage[c]] = Low;
      ellL += 1; IL += 1;
    }
    break;
  case 1:                       // sample
    assert(sat[parent]==0);
    if (parcol == Low) {
      assert(ellL>=1 && IL >= ellL);
      ll += log(chi*IL);
      ellL -= 1; IL -= 1;
    } else if (parcol == High) {
      assert(ellH>=1 && IH >= ellH);
      ll += log(chi*IH);
      ellH -= 1; IH -= 1;
    } else {
      assert(0);                // #nocov
    }
    color[parlin] = R_NaReal;
    break;
  case 2:
    assert(sat[parent]==2);
    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 (parcol == Low) {
      assert(ellL >= 1 && IL >= ellL);
      if (S >= 1 && POP > 0) {
        ll += log(Beta*S*IL/POP);
        S -= 1; IL += 1;
        ellL += 1;
        color[lineage[c1]] = Low;
        color[lineage[c2]] = Low;
      } else {
        ll += R_NegInf;
        IL += 1; ellL += 1;
        color[lineage[c1]] = Low;
        color[lineage[c2]] = Low;
      }
    } else if (parcol == High) {
      assert(ellH >= 1 && IH >= ellH);
      if (S>=1 && POP > 0) {
        ll += log(kappa*Beta*S*IH/POP);
        S -= 1; IL += 1;
        ellL += 1;
        if (unif_rand() < 0.5) {
          color[lineage[c1]] = Low;
          color[lineage[c2]] = High;
        } else {
          color[lineage[c1]] = High;
          color[lineage[c2]] = Low;
        }
        ll -= log(0.5);
    assert(!ISNAN(ll));
      } else {
        ll += R_NegInf;
        IL += 1; ellL += 1;
        color[lineage[c1]] = Low;
        color[lineage[c2]] = High;
      }
    } else {
      assert(0);                // #nocov
    }
    break;
  }
 
  // continuous portion of filter equation:
  // take Gillespie steps to the end of the interval
  if (tmax > t && R_FINITE(ll)) {
 
    double rate[nrate], logpi[nrate];
    int event;
    double event_rate = 0;
    double decay = 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 -= decay*tstep + logpi[event];
      switch (event) {
      case 0:                   // TL, s=(0,0) or s=(1,0)
        assert(S>=1 && IL>=1);
        S -= 1; IL += 1;
        ll += log(1-ellL*(ellL-1)/IL/(IL-1));
        break;
      case 1:                   // TH, s = (0,0)
        assert(S>=1 && IH >= 1);
        S -= 1; IL += 1;
        ll += log(1-ellL/IL);
        break;
      case 2:                   // TH, s=(1,0)
        assert(S>=1 && IH >= 1);
        S -= 1; IL += 1;
        change_color(color,nsample,random_choice(ellH),High,Low);
        ellH -= 1; ellL += 1;
        ll += log(1-ellH/IH/IL);
        break;
      case 3:                   // L, s=(0,0)
        assert(IL>=1);
        IL -= 1; IH += 1;
        ll += log(1-ellH/IH);
        break;
      case 4:                   // L, s=(0,1)
        assert(IL>=1);
        change_color(color,nsample,random_choice(ellL),Low,High);
        ellL -= 1; ellH += 1;
        IL -= 1; IH += 1;
        ll -= log(IH);
        break;
      case 5:                   // H, s=(0,0)
        assert(IH>=1);
        IL += 1; IH -= 1;
        ll += log(1-ellL/IL);
        break;
      case 6:                   // H, s=(1,0)
        assert(IH>=1);
        change_color(color,nsample,random_choice(ellH),High,Low);
        ellL += 1; ellH -= 1;
        IL += 1; IH -= 1;
        ll -= log(IL);
        break;
      case 7:                   // RL
        assert(IL>=1);
        IL -= 1; R += 1;
        break;
      case 8:                   // RH
        assert(IH>=1);
        IH -= 1; R += 1;
        break;
      case 9:                   // W
        assert(R>=1);
        R -= 1; S += 1;
        break;
      default:                  // #nocov
        assert(0);              // #nocov
        ll += R_NegInf;         // #nocov
        break;                  // #nocov
      }
 
      ellL = nearbyint(ellL);
      ellH = nearbyint(ellH);
 
      t += tstep;
      event_rate = EVENT_RATES;
      tstep = exp_rand()/event_rate;
 
    }
    tstep = tmax - t;
    ll -= decay*tstep;
  }
  node += 1;
}

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si2rs_rinit()

void si2rs_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, IL, IH, R plus 'ellL' and 'ellH' (numbers of L- and H-deme lineages), the accumulated weight ('ll'), the current node number ('node'), and the coloring of each lineage ('COLOR').

Definition at line 156 of file si2r_pomp.c.

  {
  double adj = POP/(S0+IL0+IH0+R0);
  S = nearbyint(S0*adj);
  IL = nearbyint(IL0*adj);
  IH = nearbyint(IH0*adj);
  R = nearbyint(R0*adj);
  ellL = 0;
  ellH = 0;
  ll = 0;
  node = 0;
}

Variable Documentation

nrate

const int nrate = 10

static

Definition at line 7 of file si2r_pomp.c.