outbreak_setup: Set up initial cases for branching process

In covid19risk/impact-sim: Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

Description

Set up initial cases for branching process

Usage

outbreak_setup(num.initial.cases, incfn, delayfn, k, prop.asym)

Arguments

num.initial.cases	Integer number of initial cases
incfn	function that samples from incubation period Weibull distribution; generated using dist_setup
delayfn	function that samples from the onset-to-hospitalisation delay Weibull distribution; generated using dist_setup
k	Numeric skew parameter for sampling the serial interval from the incubation period
prop.asym	Numeric proportion of cases that are sublinical (between 0 and 1)

Value

data.table of cases in outbreak so far

Author(s)

Joel Hellewell

Examples

## Not run: 
# incubation period sampling function
incfn <- dist_setup(dist_shape = 2.322737,dist_scale = 6.492272)
# delay distribution sampling function
delayfn <- dist_setup(delay_shape, delay_scale)
outbreak_setup(num.initial.cases = 5,incfn,delayfn,k=1.95,prop.asym=0)

## End(Not run)

covid19risk/impact-sim documentation built on April 16, 2021, 2:15 a.m.