run_scenario_Hellewell: Run scenarios as in Hellewell et al. (2020) paper
In bcgov/epi.branch.sim: Simulates an Epidemic Outbreak with a Branching Process

Description Usage Arguments Details Value

For a given tracing fraction and R0 (a "scenario"), count the fraction of simulations that are controlled. Designed to reproduce results from the source paper for this model: Hellewell et al. "Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts." The Lancet Global Health 2020; 8: E488-E496. DOI: 10.1016/S2214-109X(20)30074-7

run_scenario_Hellewell(
  nsims,
  p_trace,
  R0,
  infections_before_symptoms = "medium",
  iso_delay_length = "short",
  p_symp = 1,
  initial_cases = 20,
  max_cases = 5000
)

`nsims`	Number of simulations to run in this scenario
`p_trace`	Fraction of new infections that are traced
`R0`	Basic reproduction number for disease
`infections_before_symptoms`	One of "low", "medium" or "high" corresponding to one of three generation interval distributions considered by Hellewell et al. These distributions result in <1%, 15%, and 30% of generation interval lengths occuring prior to symptom onset. "Medium" (15%) is the default value and the benchmark used in Hellewell et al.
`iso_delay_length`	One of "short" or "long" corresponding to two distributions used by Hellewell for the delay from symptom onset to isolation for untraced symptomatic cases. "Short" is the default and benchmark value.
`p_symp`	Fraction of cases that are symptomatic. 1 is the default and benchmark value.
`initial_cases`	Number of cases at the start. 20 is the default and benchmark value
`max_cases`	Number of total cases before simulation ends with an "epidemic" outcome. Defaults to 5000, used by Hellewell et al.

The intention of this driver function is to reproduce Figure 3A from Hellewell et al. which shows the fraction of outbreaks controlled as a function of R0 and tracing fraction. These parameters are the positional arguments to this function. The remaining named arguments allow for consideration of other scenarios examined by Hellewell et al. The named arguments' default values are Hellewell et al.'s benchmark values but can be changed to reproduce results from Figure 4 of the source paper.

The secondary intention of this driver function is to provide a simple example of how to call the exported functions of this module in order to set up simulations objects, run a number of simulations and return summary statistics/metrics for further analysis.

A named vector with the following entries describing the scenario and the outcome (percentage of simulations that went extinct and absolute number of each type of outcome). Namely the entries are: nsims, R0, p_trace, percentage, nsims_extinct, nsims_epidemic, nsims_ongoing.

bcgov/epi.branch.sim documentation built on Dec. 16, 2020, 5:49 a.m.