outbreak_model: Run a single instance of the branching process model

In covid19risk/impact-sim: Feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

Description

Run a single instance of the branching process model

Usage

outbreak_model(
  num.initial.cases = NULL,
  prop.ascertain = NULL,
  cap_max_days = NULL,
  cap_cases = NULL,
  r0isolated = NULL,
  r0community = NULL,
  disp.iso = NULL,
  disp.com = NULL,
  k = NULL,
  delay_shape = NULL,
  delay_scale = NULL,
  prop.asym = NULL,
  quarantine = NULL
)

Arguments

prop.ascertain	numeric proportion of infectious contacts ascertained by contact tracing (must be 0<=x<=1)
r0isolated	numeric reproduction number for isolated cases (must be >0)
r0community	numeric reproduction number for non-isolated cases (must be >0)
disp.iso	numeric dispersion parameter for isolated cases (must be >0)
disp.com	numeric dispersion parameter for non-isolated cases (must be >0)
k	numeric skew parameter for sampling the serial interval from the incubation period
delay_shape	numeric shape parameter of delay distribution
delay_scale	numeric scale parameter of delay distribution
quarantine	logical whether quarantine is in effect, if TRUE then traced contacts are isolated before symptom onset

Value

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

Author(s)

Joel Hellewell

Examples

## Not run: 
incfn <- dist_setup(dist_shape = 2.322737,dist_scale = 6.492272)
# delay distribution sampling function
delayfn <- dist_setup(2, 4)
# generate initial cases
case_data <- outbreak_setup(num.initial.cases = 5,
                            incfn=incfn,
                            delayfn = 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,
                           r0community = 2.5,
                           prop.asym = 0,
                           incfn = incfn,
                           delayfn = delayfn,
                           prop.ascertain = 0,
                           k = 1.95,
                           quarantine = FALSE)

## End(Not run)

covid19risk/impact-sim documentation built on April 16, 2021, 2:15 a.m.