EpiBranch.jl

EpiBranch.jl is a Julia package for stochastic branching process simulation of infectious disease outbreaks. Functionality from several R packages (cf. ringbp, simulist, epichains, superspreading, pepbp) is brought together in a single package with one shared simulation engine.

The offspring draw is decoupled from timing and interventions: contacts are drawn from a branching process, generation times are assigned independently, and interventions act as competing risks on whether each contact is actually infected. For more information on the design, see Design.

Quick start

using EpiBranch
using Distributions
using StableRNGs

model = BranchingProcess(NegBin(2.5, 0.16), LogNormal(1.6, 0.5))

iso = Isolation(delay = Exponential(2.0))
ct = ContactTracing(probability = 0.5, delay = Exponential(1.5))

rng = StableRNG(42)
results = simulate_batch(model, 500;
    interventions = [iso, ct],
    attributes = clinical_presentation(incubation_period = LogNormal(1.5, 0.5)),
    sim_opts = SimOpts(max_cases = 5000),
    rng = rng,
)

containment_probability(results)

0.934

Installation

EpiBranch.jl is not yet registered. It can be installed from the repository:

using Pkg
Pkg.add(url = "https://github.com/epiforecasts/EpiBranch.jl")