outbreak_model: Run a single instance of the branching process model

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

Description

Run a single instance of the branching process model

Usage

outbreak_model(
  num.initial.cases = NULL,
  cap_gen = NULL,
  cap_max_days = NULL,
  cap_cases = NULL,
  r0isolated = NULL,
  r0community = NULL,
  disp.iso = NULL,
  disp.com = NULL,
  prop.asym = NULL,
  relR.asym = NULL,
  prop.ascertain = NULL,
  detect_sen = NULL,
  prop.presym = NULL,
  si_omega = NULL,
  incu_shape = NULL,
  incu_scale = NULL,
  delay_shape = NULL,
  delay_scale = NULL,
  delay_off = 0,
  quarant.days = NULL,
  quarant.retro.days = NULL,
  save.case_data = F
)

Arguments

num.initial.cases	number of initial cases
cap_gen	maximum number of generations to simulate
cap_max_days	maximum number of days to simulate
cap_cases	maximum number of cases to simulate
r0isolated	reproduction number of isolated cases (must be >0)
r0community	reproduction number of active cases in the community (must be >0)
disp.iso	dispersion parameter for isolated cases (must be >0)
disp.com	dispersion parameter for active cases in the community (must be >0)
prop.asym	proportion of asymptomatic cases
relR.asym	relative transmissibility of asymptomatic cases
prop.ascertain	ascertainment probability (probability of being contraced)
detect_sen	detection probability
prop.presym	proportion of pre-symptomatic transmission
si_omega	standard deviation of the generation interval
incu_shape	shape parameter of incubation period distribution
incu_scale	scale parameter of incubation period distribution
delay_shape	shape parameter of onset-to-test delay distribution
delay_scale	scale parameter of onset-to-test delay distribution
delay_off	offset of onset-to-test delay distribution
quarant.days	quarantine period (days)
quarant.retro.days	back-tracking period (days). When a contact is traced, s/he will be isolated if s/he had recall symptoms within the back-tracking period.
save.case_data	True/False (default) whether to export case line list data

Value

data.table of cases by week, cumulative cases, and the effective reproduction number of the outreak

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