run_simple_SEEIR_model: Run the SEEIR model

In mrc-ide/squire: SEIR transmission model of COVID-19

Run the SEEIR model

Description

Run the SEEIR model

Usage

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

## Not run: 
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]])

## End(Not run)

mrc-ide/squire documentation built on Sept. 10, 2022, 1:11 a.m.