R语言代码:
#example of very simple SEIR model#####
library (deSolve)
seir_model = function (current_timepoint, state_values, parameters)
{
# create state variables (local variables)
S = state_values [1] # susceptibles
E = state_values [2] # exposed
I = state_values [3] # infectious
R = state_values [4] # recovered
with (
as.list (parameters), # variable names within parameters can be used
{
# compute derivatives
dS = (-beta * S * I)
dE = (beta * S * I) - (delta * E)
dI = (delta * E) - (gamma * I)
dR = (gamma * I)
# combine results
results = c (dS, dE, dI, dR)
list (results)
}
)
}
contact_rate = 10 # number of contacts per day
transmission_probability = 0.07 # transmission probability
infectious_period = 5 # infectious period
latent_period = 21 # latent period
beta_value = contact_rate * transmission_probability
gamma_value = 1 / infectious_period
delta_value = 1 / latent_period
Ro = beta_value / gamma_value
parameter_list = c (beta = beta_value, gamma = gamma_value, delta = delta_value)
V = 5000 # exposed hosts
X = 9999 # susceptible hosts
Y = 1 # infectious hosts
Z = 0 # recovered hosts
N = V + X + Y + Z
initial_values = c (S = X/N, E = V/N, I = Y/N, R = Z/N)
timepoints = seq (0, 50, by=1)
output = lsoda (initial_values, timepoints, seir_model, parameter_list)