pf_outbreak_step: Move forward one generation in the branching process

In dachuwu/DTQbp: A package for modeling case detection, contact tracing and quarantine with branching processes

Description

Move forward one generation in the branching process

Usage

pf_outbreak_step(
  case_data = NULL,
  r0symp = NULL,
  disp.com = NULL,
  disp.iso = NULL,
  r0isolated = NULL,
  prop.asym = NULL,
  relR.asym = NULL,
  prop.ascertain = NULL,
  quarant.days = NULL,
  quarant.retro.days = NULL,
  incfn = NULL,
  delayfn = NULL,
  inf_fn = NULL
)

Arguments

case_data	data.table of cases in outbreak so far; initially generated by outbreak_setup
r0symp	numeric reproduction number for non-isolated cases (must be >0)
disp.com	numeric dispersion parameter for non-isolated cases (must be >0)
disp.iso	numeric dispersion parameter for isolated cases (must be >0)
r0isolated	numeric reproduction number for isolated cases (must be >0)
prop.ascertain	numeric proportion of infectious contacts ascertained by contact tracing (must be 0<=x<=1)
quarant.days	quarantine days
quarant.retro.days	batracking of symptom onset
incfn	function samples from incubation period; generated by dist_setup
delayfn	function samples from the onset-to-hospitalisation delay; generated by dist_setup
k	numeric skew parameter for sampling the serial interval from the incubation period

Author(s)

Joel Hellewell

dachuwu/DTQbp documentation built on Dec. 19, 2021, 8:01 p.m.