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RIVM_SIR_formulas_values.txt
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# FORMULAS AND VALUES TO MAKE A SIR MODEL FOR THE NETHERLANDS
# SOURCE : RIVM https://www.rivm.nl/sites/default/files/2021-03/Modellingresults%20COVID19%20vaccination%20version1.0%2020210324_0.pdf
# retreived 21st of April 2021
# Copied by René SMIT
# Fouten voorbehoude
R0 = 2.3 # basic reproduction number
Reff = 1.04 # effective reproduction number
beta = 0.00061 # transmission rate
sigma = 0.5 # inverse of latent period
gamma = 0.5 # inverse of infectious period
lambda = beta * ( C * (( I + Iv1d + Iv2d) / N)) # force of infection
alfa = 3.5/17.5 # rate of vaccination with the first dose
alfa2 = 1/17.4 # UNKNOWN # rate of vaccination with the second dose
delta = 14 # TABLE2 # delay to protection of first dose
delta2 = 14 #TABLE2 # delay of protection of second dose
eta = 0.2 # 1- vacc_eff_first_dose # SEE TABLE 2
eta2 = 0.2 # 1- vacc_eff_sec_dose # # SEE TABLE 2
dSdt = -lambda * S - alfa * S
dShold1ddt =alfa * S - (1/delta)* Shold1d - lambda* Shold1d
dSv1ddt= (1/delta) * Shold1d - eta * lamda * Sv1d - alfa2 * Sv1d
dShold2ddt = alfa2 * Sv1d - (1/delta2)*Shold2d - eta * lambda * Shold2d
dSv2ddt = (1/delta2) * Shold2d - eta2 * lamda * Sv2d
DEdt = lambda * (S + Shold1d) - sigma * E
dEv1ddt = eta * lamda * (Sv1d+Shold2d) - sigma * Ev1d
dEv2ddt = eta2 * lambda * Sv2d - sigma * Ev2d
dIdt = sigma * E - (gamma + h)*I
dIdv1ddt = sigma * Ev1d - (gamma + h)*Iv1d
dIv2ddt = sigma * Ev2d- (gamma + h)*Iv2d
dHdt = h*I - (i1 +d +r) *H
dHv1ddt = h*Iv1d- (i1+d+r)*Hv1d
dHv2ddt = h*Iv2d- (i1+d+r)*Hv2d
dICdt = i1*H - (i2+dic)*IC
dICv1ddt = i1*Hv1d - (i2+dic)*ICv1d
dICv2ddt = i1*Hv2d - (i2+dic)*ICv2d
dHICdt = i2 * IC - (ric+dhic)*HIC
dHICv1ddt = i2 * ICv1d - (ric+dhic)*HICv1d
dHICv2ddt = i2 * ICv2d - (ric+dhic)*HICv2d
dDdt = d* (H + v1d+ Hv2d) + dic * (IC +ICv1d + ICv2d) + dhic * (HIC + HICv1d + HICv2d)
dRdt = gamma * I + r* H + ric + HIC
dRv1ddt = gamma * Iv1d + r* Hv1d + ric + HICv1d
dRv2ddt = gamma * Iv1d + r* Hv1d + ric + HICv2d
daily_infections = S + hold1d + (eta * (Sv1d + Shold2d)) + (eta2 * Sv2d)) * lambda
daily_cases = sigma * (E + Ev1d + Ev2d) * P(ascertainment)
hospital_admissions = (I + Iv1d +Iv2d) * h
ic_admissions = (H + Hv1d + Hv2d) * i1
daily_deaths = (H + Hv1d + Hv2d) * d + (IC + ICv1d + ICv2d) * dIC + (HIC+ HICv1d + HICv2d) * hIC
life_years_lost = deaths * life_expectancy
# 0-9 10-19 20-29 30-39 40-49 50-59 60-69 70-79 80+
pop = [1756000, 1980000, 2245000, 2176000, 2164000, 2548000, 2141000, 1615000, 839000]
fraction = [0.10055, 0.11338, 0.12855, 0.12460, 0.12391, 0.14590, 0.12260, 0.09248, 0.04804]
h = [0.0015, 0.0001, 0.0002, 0.0007, 0.0013, 0.0028, 0.0044, 0.0097, 0.0107] # I -> H
i1 = [0.0000, 0.0271, 0.0422, 0.0482, 0.0719, 0.0886, 0.0170, 0.0860, 0.0154] # H-> IC
i2 = [0.0555, 0.0555, 0.0555, 0.0555, 0.0555, 0.0531, 0.0080, 0.0367, 0.0356] # IC-> H
d = [0.0003, 0.0006, 0.0014, 0.0031, 0.0036, 0.0057, 0.0151, 0.0327, 0.0444] # H-> D
dic = [0.0071, 0.0071, 0.0071, 0.0071, 0.0071, 0.0090, 0.0463, 0.0225, 0.0234] # IC -> D
dhic = [0.0000, 0.0000, 0.0000, 0.0000, 0.0000, 0.0010, 0.0040, 0.0120, 0.0290] # IC -> h -> D
r = [0.1263, 0.1260, 0.1254, 0.1238, 0.1234, 0.1215, 0.1131, 0.0976, 0.08720 # recovery rate from hospital (before IC)
ric = [0.0857, 0.0857, 0.0857, 0.0857, 0.0857, 0.0821, 0.0119, 0.0567, 0.0550] # recovery rate from hospital (after IC)
LE = [ 77.89, 67.93, 58.08, 48.48, 38.60, 29.22, 20.52, 12.76, 4.35 ] # Life expectancy
RSI = [ 1.000, 3.051, 5.751, 3.538, 3.705, 4.365, 5.688, 5.324, 7.211] # Relative suspceptibility/infectiousness
# name = [ delay to protection, vaccin efficacy] # aantal gezet 18 april
pfizer1 = [14, 92.6] # 2954000
pfizer2 = [7, 94.8]
moderna1 = [14, 89.6] # 323000
moderna2 = [14, 94.1]
astrazenica1 = [21, 58.3] # 1322000
astrazenica2 = [14, 62.1]
janssen = [14, 66.1] # 0