// Created by libAntimony v2.8.0
model *restif07()
// Compartments and Species:
compartment env;
substanceOnly species N in env, S in env, I1 in env, I2 in env, R1 in env;
substanceOnly species R2 in env, V in env, Iv2 in env, J2 in env, J1 in env;
substanceOnly species R in env;
// Assignment Rules:
mu := 1/l_e;
beta := R0*(gamma + mu);
gamma := 365/tInf;
sigma := 1/tImm;
sigmaV := 1/tImm_V;
strain1_frac := (I1 + J1)/N;
strain2_frac := (I2 + J2 + Iv2)/N;
S_frac := S/N;
V_frac := V/N;
R_1_frac := (R1 + R)/N;
R_2_frac := (R2 + R)/N;
R_frac := R/N;
// Reactions:
r1: => S; mu*(1 - p)*N;
r2: => V; mu*p*N;
r3: S => ; mu*S;
r4: V => ; mu*V;
r5: I1 => ; mu*I1;
r6: I2 => ; mu*I2;
r7: Iv2 => ; mu*Iv2;
r8: R1 => ; mu*R1;
r9: R2 => ; mu*R2;
r10: J1 => ; mu*J1;
r11: J2 => ; mu*J2;
r12: R => ; mu*R;
r13: S => I1; beta*S*((I1 + J1)/N);
r14: S => I2; beta*S*((I2 + J2 + Iv2)/N);
r15: V => Iv2; beta*(1 - tau)*V*((I2 + J2 + Iv2)/N);
r16: I1 => R1; gamma*I1;
r17: I2 => R2; gamma*I2;
r18: R2 => J1; (beta*(1 - theta)*R2*(I1 + J1))/N;
r19: R1 => J2; (beta*(1 - theta)*R1*(I2 + J2 + Iv2))/N;
r20: J1 => R; gamma/(1 - nu)*J1;
r21: J2 => R; gamma/(1 - nu)*J2;
r22: Iv2 => R; gamma/(1 - eta)*Iv2;
r23: R1 => S; sigma*R1;
r24: R2 => S; sigma*R2;
r25: R => S; sigma*R;
r26: V => S; sigmaV*V;
// Species initializations:
N = 1/env;
S = 0.0588235/env;
I1 = 0.00176967/env;
I2 = 1e-006/env;
R1 = 0.439407/env;
R2 = 0;
V = 0.9/env;
Iv2 = 0.5/env;
J2 = 0;
J1 = 0;
R = 0;
// Compartment initializations:
env = 1;
mu has per_year;
// Variable initializations:
l_e = 50;
l_e has time_unit;
beta has per_year;
R0 = 17;
R0 has dimensionless;
gamma has per_year;
tInf = 21;
tInf has day;
p = 1;
p has dimensionless;
tau = 0.7;
tau has dimensionless;
theta = 0.5;
theta has dimensionless;
nu = 0.5;
nu has dimensionless;
eta = 0.5;
eta has dimensionless;
sigma has per_year;
tImm = 20;
tImm has time_unit;
sigmaV has per_year;
tImm_V = 50;
tImm_V has time_unit;
strain1_frac has dimensionless;
strain2_frac has dimensionless;
S_frac has dimensionless;
V_frac has dimensionless;
R_1_frac has dimensionless;
R_2_frac has dimensionless;
R_frac has dimensionless;
// Other declarations:
var mu, beta, gamma, sigma, sigmaV, strain1_frac, strain2_frac, S_frac;
var V_frac, R_1_frac, R_2_frac, R_frac;
const env, l_e, R0, tInf, p, tau, theta, nu, eta, tImm, tImm_V;
// Unit definitions:
unit substance = item;
unit time_unit = 3.1536e+007 second;
unit day = 86400 second;
unit per_year = 1 / 3.1536e+007 second;
// Display Names:
substance is "individuals";
time_unit is "years";
day is "days";
env is "environment";
l_e is "life expectancy";
tInf is "infectious period (d)";
tImm is "immune period (yr)";
tImm_V is "vaccine immune period (yr)";
r1 is "Birth S (unvaccinated)";
r2 is "Birth V (vaccinated)";
r3 is "Death in S";
r4 is "Death in V";
r5 is "Death in I1";
r6 is "Death in I2";
r7 is "Death in Iv2";
r8 is "Death in R1";
r9 is "Death in R2";
r10 is "Death in J1";
r11 is "Death in J2";
r12 is "Death in Rp";
r13 is "Primary Infection with strain 1";
r14 is "Primary Infection with strain 2";
r15 is "Primary Infection of V with strain 2";
r16 is "Recovery (I1)";
r17 is "Recovery (I2)";
r18 is "Secondary Infection with strain 1";
r19 is "Secondary Infection with strain 2";
r20 is "Recovery (J1)";
r21 is "Recovery (J2)";
r22 is "Recovery (Iv2)";
r23 is "Loss of Immunity (R1)";
r24 is "Loss of Immunity (R2)";
r25 is "Loss of Immunity (Rp)";
r26 is "Loss of Immunity (V)";
end