Move forward one generation in the branching process

outbreak_step(
  case_data = NULL,
  disp.iso = NULL,
  disp.com = NULL,
  r0isolated = NULL,
  r0community = NULL,
  prop.asym = NULL,
  incfn = NULL,
  delayfn = NULL,
  prop.ascertain = NULL,
  k = NULL,
  quarantine = NULL,
  r0subclin = NULL,
  disp.subclin = NULL
)

Arguments

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 cases that are completely asymptomatic.
incfn: function samples from incubation period; generated by dist_setup
delayfn: function samples from the onset-to-hospitalisation delay; generated by dist_setup
prop.ascertain: numeric proportion of infectious contacts ascertained by contact tracing (must be 0<=x<=1)
k: numeric 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
r0subclin: numeric reproduction number for sub-clinical non-isolated cases (must be >0)
disp.subclin: numeric dispersion parameter for sub-clincial non-isolated cases (must be >0)

Author

Joel Hellewell

Examples


if (FALSE) {
# incubation period sampling function
incfn <- dist_setup(dist_shape = 2.322737,dist_scale = 6.492272)
# delay distribution sampling function
delayfn <- dist_setup(1.651524, 4.287786)
# 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 = case_data,
disp.iso = 1,
disp.com = 0.16,
r0isolated = 0,
r0subclin = 1.25,
disp.subclin = 0.16,
r0community = 2.5,
prop.asym = 0,
incfn = incfn,
delayfn = delayfn,
prop.ascertain = 0,
k = 1.95,
quarantine = FALSE)[[1]]
}