/* this is for the model where parasites "eat" reserves */
void derivs (int *neq, double *t, double *y, double *ydot) {
// fixed parameters whose values will not ever vary
double eps = 0.00000000816536; // carbon content of algae from Meg's data
double V = 30; // volume of the container
double xi = 0.0018; // length-weight regression coefficient from Spencer
double q = 3; // length-weight regression exponent from Spencer
// foraging-dependent parameters
double Fh = 12000; // half-saturation constant
double Imax = 12162; // ingestion rate
double g = 1.467; // size-dependence of ingestion
double a = 3.2e-5; // spore coefficient
double h = 3.57; // size -dependence of spore dependence
// state variables
double F = y[0]; // algal concentration
double E = y[1]; // energy reserves
double W = y[2]; // structural weight
double Pi = y[3]; // immature parasites
double Pm = y[4]; // mature parasites
double L = pow(W, 1/3); // structural length
double Lobs = pow(W/xi, 1/q); //observed length
// ingestion
double ing = Imax * F/(Fh+F) * pow(Lobs,g) * exp(-a * Pm/pow(Lobs,h));
// mobilization
double pc = E * (v/L + km) / (1 + K*E/W);
// total number of state variables
int Nout = 5;
// which state variables do we want
int nr[5] = {0, 1, 2, 3, 4};
// array of initial values
double ytau[5] = {0.0, 0.0, 0.0, 0.0, 0.0};
double T = *t - tau;
if (*t > tau) {
lagvalue(T, nr, Nout, ytau);
}
// balance the equations
ydot[0] = -ing;
ydot[1] = rho*eps*V*ing - pc;
ydot[2] = K*pc - km*W - aP*W*Pi;
ydot[3] = eP*aP*W/(hP+W)*Pi - exp(-m*tau)*eP*aP*ytau[2]/(hP+ytau[2])*ytau[3] - m*Pi;
ydot[4] = exp(-m*tau)*eP*aP*ytau[2]/(hP+ytau[2])*ytau[3];
}
/* Derivatives */
void derivs (int *neq, double *t, double *y, double *ydot,
double *yout, int *ip) {
if (ip[0] < 1) error("nout should be at least 1");
int nr[1] = {0}; // which lags are needed?
// numbering starts from zero !
double ytau[1] = {1.0}; // array; initialize with default values !
double T = *t - tau;
if (*t > tau) {
lagvalue(T, nr, 1, ytau);
//Rprintf("test %g %g %g \n", T, y[0], ytau[0]);
}
yout[0] = ytau[0];
ydot[0] = k * ytau[0];
}
