outbreak_setup: Set up initial cases for branching process
In emmalouisedavis/TTI-branching-process: TTI COVID-19 branching process model

Description Usage Arguments Value Author(s) Examples

Set up initial cases for branching process

outbreak_setup(
  num.initial.cases,
  incfn,
  delayfn,
  prop.asym,
  sensitivity,
  precaution,
  test_delay,
  self_report,
  testing
)

`num.initial.cases`	Integer number of initial cases
`incfn`	function that samples from incubation period Weibull distribution; generated using dist_setup
`delayfn`	function generated using dist_setup = 1 or Inf (adherence to isolation)
`prop.asym`	Numeric proportion of cases that are sublinical (between 0 and 1)
`sensitivity`	Test sensitivity.
`precaution`	After a negative test result, keep people in quarantine for this long as a precautionary measure.
`test_delay`	How long does it take for tests to be administered and results returned.
`self_report`	Probability that someone that is not tracked will self report (111 for example) after symptoms.
`testing`	Logical to determine whether testing is used.

data.table of cases in outbreak so far

Emma Davis and Tim Lucas (from Joel Hellewell)

## 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)