Public
Edited
Jun 6, 2023
plotKeys(["S","I","R","newI",d=>d.vax.S, d=>d.S - d.vax.S], false, dataWithVax,["S","I","R","newI","S vaxed", "S unvaxed"]);
plotKeys([d=>d.newI/d.N,d=>d.vax.newI/d.vax.N, d=>(d.newI - d.vax.newI)/(d.N - d.vax.N)], false, dataWithVax,["Infection rate total", "Infection rate vaxed", "Infection rate unvaxed"]);
plotKeys([d=>d.vax.newI/d.vax.N/((d.newI - d.vax.newI)/(d.N - d.vax.N))], false, dataWithVax,[" "]);
function genSIR(initial = {}, n = 150, intervention = {}) {
let N = 1000;
const defaultInitial = {
Day: 0,
S:N-1,
I:1,
Infected:1,
R:0,
N:N,
cumulativeI: 1,
Infected: 0,
gamma: .25,
beta: beta,
incubation:1,
};
const defaultIntervention = {
firstDay: 30,
duration: 7,
gamma: 0.45,
beta: beta,
importedCases: 0,
importedCasesDay: 0,
vaccinated: 0,
vaccineEffectivenessAgainstInfection: 0,
};
initial = {...defaultInitial,...initial};
intervention = {...defaultInitial,...defaultIntervention, ...intervention};
if (intervention.vaccinated) {
initial.vax = {
S: intervention.vaccinated,
I: 0,
R: 0,
N: intervention.vaccinated,
cumulativeI: 0,
Infected: 0,
gamma: .25,
beta: beta,
incubation:1,
};
}
else {
initial.vax = {};
}
const a = [initial];
for (let i = 1 ; i <= n ; i++) {
let p = a[i-1];
let interventionActive = i >= intervention.firstDay && i < intervention.firstDay + intervention.duration;
let active = interventionActive ? intervention : initial ;
let incubation = active.incubation;
let pi = a[Math.max(i-incubation,0)];
console.log(incubation,pi);
let beta = active.beta ;
let gamma = active.gamma ;
let Reff = active.beta * p.S / p.N / active.gamma ;
let newI = active.beta * pi.I * p.S / p.N;
let vax = {
...p.vax,
gamma,
beta,
};
if (intervention.vaccinated) {
let ve = i < intervention.vaccinationDay ? 0 : intervention.vaccineEffectivenessAgainstInfection ;
newI -= active.beta * ve * pi.I * vax.S / p.N;
let newIvax = active.beta * (1-ve) * pi.I * vax.S / p.N;
let newRvax = active.gamma * vax.I;
vax.I += newIvax - newRvax;
vax.R += newRvax ;
vax.S -= newIvax;
vax.Infected = vax.I + vax.R;
vax.newI = newIvax;
vax.cumulativeI += newIvax;
}
if (intervention.importedCasesDay === i) {
newI += importedCasesInfectiousness*Reff*intervention.importedCases ;
}
let newR = active.gamma * p.I;
let I = p.I + newI - newR ;
let R = p.R + newR;
a[i] = {
...p,
vax,
gamma,
beta,
Day: i,
S: p.S - newI,
I,
R,
Reff,
newI,
Infected: I + R,
cumulativeI: p.cumulativeI + newI,
};
}
return a;
}
data = genSIR({
gamma: initialGamma,
incubation: incubationPeriod,
},200,{
firstDay: interventionStart,
duration: interventionDays,
gamma: interventionGamma,
});
dataImportedCases = genSIR({
gamma: initialGamma,
incubation: incubationPeriod,
},200,{
firstDay: interventionStart,
duration: interventionDays,
gamma: interventionGamma,
importedCases,
importedCasesDay,
importedCasesInfectiousness,
});
dataWithVax = genSIR({
gamma: initialGamma,
incubation: incubationPeriod,
},200,{
firstDay: 0,
duration: 0,
gamma: initialGamma,
vaccinated,
vaccineEffectivenessAgainstInfection,
vaccinationDay,
});
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Observable is your go-to platform for exploring data and creating expressive data visualizations. Use reactive JavaScript notebooks for prototyping and a collaborative canvas for visual data exploration and dashboard creation.
