run_simple_SEEIR_model.Rd
Run the SEEIR model
run_simple_SEEIR_model(
R0 = 3,
tt_R0 = 0,
dt = 0.1,
init = NULL,
dur_E = 4.58,
dur_I = 2.09,
day_return = FALSE,
population,
contact_matrix_set,
tt_contact_matrix = 0,
time_period = 365,
replicates = 10
)
R0 | Basic reproduction number |
---|---|
tt_R0 | Change time points for R0 |
dt | Time step |
init | Data.frame of initial conditions |
dur_E | Mean duration of incubation period (days) |
dur_I | Mean duration of infectious period (days) |
day_return | Logical, do we want to return outut after each day rather than each dt. Default = FALSE |
population | Population vector (for each age group) |
contact_matrix_set | Contact matrices used in simulation |
tt_contact_matrix | Time change points for matrix change |
time_period | Length of simulation |
replicates | Number of replicates |
Simulation output
if (FALSE) {
pop <- get_population("Afghanistan", simple_SEIR = TRUE)
m1 <- run_simple_SEEIR_model(population = pop$n, dt = 1,
R0 = 2,
contact_matrix_set=contact_matrices[[1]])
}