Set up initial cases for branching process

Source: R/outbreak_setup.R

Set up initial cases for branching process

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

Joel Hellewell

Examples


if (FALSE) {
# 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)
}