Outbreak simulation based on a branching process
Simulate outbreaks of a communicable disease. This is both a simulation framework and an implementation that uses very simplistic modelling assumptions.
This is a Rust library, and can be added to your Cargo.toml with:
[dependencies]
obsim = { git = "https://github.com/cidm-ph/obsim" }See the development documentation.
You do not necessarily need to be familiar with Rust to make use of this
library as it comes with some examples that you can modify.
See Installing Rust to get set up.
With the repository checked out, you can edit the configuration in the examples
and then e.g. cargo run --example simple > simulation.fa to get an annotated
FASTA file with the simulation result.
The currently implemented models are too simplistic to capture many real features of microbial evolution. They are intended for simple approximations that apply on short timescales where only a few mutations are expected to occur over the duration of outbreaks.
The framework can be extended with more sophisticated models using the same simple interfaces to drive simulations.
This framework was created for the following study
Suster CJE, Arnott A, Blackwell G, Gall M, Draper J, Martinez E, Drew AP, Rockett RJ, Chen SC-A, Kok J, Dwyer DE and Sintchenko V (2022) Guiding the design of SARS-CoV-2 genomic surveillance by estimating the resolution of outbreak detection. Front. Public Health 10:1004201. doi: 10.3389/fpubh.2022.1004201
Dual-licensed under MIT or Apache 2.0.
© 2022 Western Sydney Local Health District, NSW Health