simpleSim: Simple SIR simulation

In jrcpulliam/LLsim: Line List Simulator

Description

simpleSim runs a stochastic SIR model with gamma-distributed waiting times.

Usage

simpleSim(
  inc_mean_param,
  inf_mean_param,
  R_0,
  case_fatality,
  pop_size,
  inc_shape_param = 1,
  inf_shape_param = 1,
  initial_cases = 1,
  max_time = 365,
  seed = 20200129
)

Arguments

inc_mean_param	Mean of the incubation period distribution
inf_mean_param	Mean of the infectious period
R_0	Basic reproductive number
case_fatality	Proportion of cases that die
pop_size	Size of the population
inc_shape_param	Shape parameter of the incubation period distribution (default = 1)
inf_shape_param	Shape parameter of the infectious period distribution (default = 1)
initial_cases	Initial number of cases (default = 1)
max_time	Maximum time for the simulation to run (default = 365)
seed	Seed for the random number generator (default = 20200129)

Details

TODO: Add more details later

Value

Returns a list with two dataframes: pop, the full population on which the simulation was run, and cases a preliminary line list (perfect reporting)

TODO: Add more detail

jrcpulliam/LLsim documentation built on Feb. 5, 2020, 8:49 p.m.