#include <Rmath.h>
#include "pomp.h"

Include dependency graph for gompertz.c:

Macros
#define	R (p[parindex[0]])

#define	K (p[parindex[1]])

#define	SIGMA (p[parindex[2]])

#define	TAU (p[parindex[3]])

#define	Y (y[obsindex[0]])

#define	X (x[stateindex[0]])

#define	XPRIME (f[stateindex[0]])

#define	EY (f[obsindex[0]])

#define	VY (f[vmatindex[0]])

#define	r (__p[__parindex[0]])

#define	K (__p[__parindex[1]])

#define	sigma (__p[__parindex[2]])

#define	tau (__p[__parindex[3]])

#define	X_0 (__p[__parindex[4]])

#define	T_r (__pt[__parindex[0]])

#define	T_K (__pt[__parindex[1]])

#define	T_sigma (__pt[__parindex[2]])

#define	T_tau (__pt[__parindex[3]])

#define	T_X_0 (__pt[__parindex[4]])

Functions
void	_gompertz_normal_dmeasure (double lik, double y, double x, double p, int give_log, int obsindex, int stateindex, int parindex, int covindex, double *covars, double t)

void	_gompertz_normal_rmeasure (double y, double x, double p, int obsindex, int stateindex, int parindex, int covindex, double covars, double t)

void	_gompertz_normal_emeasure (double f, double x, double p, int obsindex, int stateindex, int parindex, int covindex, double covars, double t)

void	_gompertz_normal_vmeasure (double f, double x, double p, int vmatindex, int stateindex, int parindex, int covindex, double covars, double t)

void	_gompertz_step (double x, const double p, const int stateindex, const int parindex, const int covindex, const double covar, double t, double deltat)

void	_gompertz_skeleton (double f, double x, const double p, const int stateindex, const int parindex, const int covindex, const double *covar, double t)

void	_gompertz_to_trans (double __pt, const double __p, const int *__parindex)

void	_gompertz_from_trans (double __p, const double __pt, const int *__parindex)

Macro Definition Documentation

◆ EY

#define EY (f[obsindex[0]])

Definition at line 16 of file gompertz.c.

◆ K [1/2]

#define K (p[parindex[1]])

Definition at line 9 of file gompertz.c.

◆ K [2/2]

#define K (__p[__parindex[1]])

Definition at line 9 of file gompertz.c.

◆ R

#define R (p[parindex[0]])

Definition at line 8 of file gompertz.c.

◆ r

#define r (__p[__parindex[0]])

Definition at line 91 of file gompertz.c.

◆ SIGMA

#define SIGMA (p[parindex[2]])

Definition at line 10 of file gompertz.c.

◆ sigma

#define sigma (__p[__parindex[2]])

Definition at line 93 of file gompertz.c.

◆ T_K

#define T_K (__pt[__parindex[1]])

Definition at line 97 of file gompertz.c.

◆ T_r

#define T_r (__pt[__parindex[0]])

Definition at line 96 of file gompertz.c.

◆ T_sigma

#define T_sigma (__pt[__parindex[2]])

Definition at line 98 of file gompertz.c.

◆ T_tau

#define T_tau (__pt[__parindex[3]])

Definition at line 99 of file gompertz.c.

◆ T_X_0

#define T_X_0 (__pt[__parindex[4]])

Definition at line 100 of file gompertz.c.

◆ TAU

#define TAU (p[parindex[3]])

Definition at line 11 of file gompertz.c.

◆ tau

#define tau (__p[__parindex[3]])

Definition at line 94 of file gompertz.c.

◆ VY

#define VY (f[vmatindex[0]])

Definition at line 17 of file gompertz.c.

◆ X

#define X (x[stateindex[0]])

Definition at line 14 of file gompertz.c.

◆ X_0

#define X_0 (__p[__parindex[4]])

Definition at line 95 of file gompertz.c.

◆ XPRIME

#define XPRIME (f[stateindex[0]])

Definition at line 15 of file gompertz.c.

◆ Y

#define Y (y[obsindex[0]])

Definition at line 13 of file gompertz.c.

Function Documentation

◆ _gompertz_from_trans()

void _gompertz_from_trans	(	double *	__p,
		const double *	__pt,
		const int *	__parindex
	)

Definition at line 113 of file gompertz.c.

   {
  r = exp(T_r);
  K = exp(T_K);
  sigma = exp(T_sigma);
  tau = exp(T_tau);
  X_0 = exp(T_X_0);
}

◆ _gompertz_normal_dmeasure()

void _gompertz_normal_dmeasure	(	double *	lik,
		double *	y,
		double *	x,
		double *	p,
		int	give_log,
		int *	obsindex,
		int *	stateindex,
		int *	parindex,
		int *	covindex,
		double *	covars,
		double	t
	)

Definition at line 20 of file gompertz.c.

   {
  *lik = dlnorm(Y,log(X),TAU,give_log);
}

◆ _gompertz_normal_emeasure()

void _gompertz_normal_emeasure	(	double *	f,
		double *	x,
		double *	p,
		int *	obsindex,
		int *	stateindex,
		int *	parindex,
		int *	covindex,
		double *	covars,
		double	t
	)

Definition at line 40 of file gompertz.c.

   {
  EY = X*exp(TAU*TAU/2);
}

◆ _gompertz_normal_rmeasure()

void _gompertz_normal_rmeasure	(	double *	y,
		double *	x,
		double *	p,
		int *	obsindex,
		int *	stateindex,
		int *	parindex,
		int *	covindex,
		double *	covars,
		double	t
	)

Definition at line 30 of file gompertz.c.

   {
  Y = rlnorm(log(X),TAU);
}

◆ _gompertz_normal_vmeasure()

void _gompertz_normal_vmeasure	(	double *	f,
		double *	x,
		double *	p,
		int *	vmatindex,
		int *	stateindex,
		int *	parindex,
		int *	covindex,
		double *	covars,
		double	t
	)

Definition at line 50 of file gompertz.c.

                                                          {
  double et = exp(TAU*TAU);
  VY = X*X*et*(et-1);
}

◆ _gompertz_skeleton()

void _gompertz_skeleton	(	double *	f,
		double *	x,
		const double *	p,
		const int *	stateindex,
		const int *	parindex,
		const int *	covindex,
		const double *	covar,
		double	t
	)

Definition at line 70 of file gompertz.c.

   {
  double deltat = 1.0;
  double S = exp(-R*deltat);
  XPRIME = R_pow(K,1-S)*R_pow(X,S); // X is not over-written in the skeleton function
}

◆ _gompertz_step()

void _gompertz_step	(	double *	x,
		const double *	p,
		const int *	stateindex,
		const int *	parindex,
		const int *	covindex,
		const double *	covar,
		double	t,
		double	deltat
	)

Definition at line 58 of file gompertz.c.

   {
  double S = exp(-R*deltat);
  double eps = (SIGMA > 0.0) ? exp(rnorm(0,SIGMA)) : 1.0;
  X = R_pow(K,1-S)*R_pow(X,S)*eps; // note X is over-written by this line
}

◆ _gompertz_to_trans()

void _gompertz_to_trans	(	double *	__pt,
		const double *	__p,
		const int *	__parindex
	)

Definition at line 102 of file gompertz.c.

   {
  T_r = log(r);
  T_K = log(K);
  T_sigma = log(sigma);
  T_tau = log(tau);
  T_X_0 = log(X_0);
}

Macros

Functions