outbreak_step: Move forward one generation in the branching process
In emmalouisedavis/TTI-branching-process: TTI COVID-19 branching process model

Description Usage Arguments Value Author(s)

Move forward one generation in the branching process

outbreak_step(
  case_data,
  disp.iso,
  disp.com,
  r0isolated,
  r0community,
  prop.asym,
  incfn,
  delayfn,
  inf_rate,
  inf_shape,
  inf_shift,
  prop.ascertain,
  min_quar_delay,
  max_quar_delay,
  test_delay,
  sensitivity,
  precaution,
  self_report,
  quarantine,
  testing
)

`case_data`	data.table of cases in outbreak so far; initially generated by outbreak_setup
`disp.iso`	numeric dispersion parameter for isolated cases (must be >0)
`disp.com`	numeric dispersion parameter for non-isolated cases (must be >0)
`r0isolated`	numeric reproduction number for isolated cases (must be >0)
`r0community`	numeric reproduction number for non-isolated cases (must be >0)
`prop.asym`	Proportion of asymptomatics.
`incfn`	function samples from incubation period; generated by dist_setup
`delayfn`	function samples adherence and delay to isolation
`inf_rate`	Rate parameter for the gamma distribution of serial intervals around the symptom onset distribution.
`inf_shape`	The shape for the gamma distribution of serial intervals around the symptom onset distribution.
`inf_shift`	Shift the gamma distribution of serial intervals around the symptom onset distribution back by this much (i.e. transmission can ocur this much before symptom onset).
`prop.ascertain`	numeric proportion of infectious contacts ascertained by contact tracing (must be 0<=x<=1)
`min_quar_delay`	The minimum delay between a case being identified and their contacts being isolated (only applies when quarentine set to TRUE)
`max_quar_delay`	The maximum delay between a case being identified and their contacts being isolated (only applies when quarentine set to TRUE)
`test_delay`	How long does it take for tests to be administered and results returned.
`sensitivity`	Test sensitivity.
`precaution`	After a negative test result, keep people in quarantine for this long as a precautionary measure.
`self_report`	Probability that someone that is not tracked will self report (111 for example) after symptoms.
`quarantine`	logical whether quarantine is in effect, if TRUE then traced contacts are isolated before symptom onset
`testing`	Logical to determine whether testing is used.