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

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	reproduction number for non-isolated cases (must be >0)
disp.com	dispersion parameter for non-isolated cases (must be >0)
disp.iso	dispersion parameter for isolated cases (must be >0)
r0isolated	reproduction number for isolated cases (must be >0)
prop.ascertain	proportion of infectious contacts ascertained by contact tracing (must be 0<=x<=1)
incfn	(function) samples from incubation period; generated by dist_setup
delayfn	(function) samples from the onset-to-hospitalisation delay; generated by dist_setup
k	skew parameter for sampling the serial interval from the incubation period
quarantine	(logical) whether quarantine is in effect, if TRUE then traced contacts are isolated before symptom onset

Author(s)

Joel Hellewell

Examples

## 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)
# generate initial cases
case_data <- outbreak_setup(num.initial.cases = 5,incfn,delayfn,k=1.95,prop.asym=0)
# generate next generation of cases
case_data <- outbreak_step(case_data,1,0.16,0,2.5,0,incfn,delayfn,0,1.95,FALSE)

## End(Not run)

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