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
)

Arguments

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

Value

Simulation output

Examples

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]])
}