JUNE: open-source individual-based epidemiology simulation
This is the offical repository of JUNE, named after June Almeida, who was the female Scottish virologist that first identified the coronavirus group of viruses. A paper introducing our modelling framework in the case of modelling the spread of COVID-19 in England has been published in Royal Society Open Science.
Please cite our paper as follows:
@article{doi:10.1098/rsos.210506,
author = {Aylett-Bullock, Joseph and Cuesta-Lazaro, Carolina and Quera-Bofarull, Arnau and Icaza-Lizaola, Miguel and Sedgewick, Aidan and Truong, Henry and Curran, Aoife and Elliott, Edward and Caulfield, Tristan and Fong, Kevin and Vernon, Ian and Williams, Julian and Bower, Richard and Krauss, Frank },
title = {June: open-source individual-based epidemiology simulation},
journal = {Royal Society Open Science},
volume = {8},
number = {7},
pages = {210506},
year = {2021},
doi = {10.1098/rsos.210506},
URL = {https://royalsocietypublishing.org/doi/abs/10.1098/rsos.210506},
eprint = {https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.210506},
}
To reproduce the plots to that paper vist our paper plots repository.
Setup
The easiest way to get JUNE up and running is to install the latest stable version,
pip install june
and download the data by running the command
get_june_data.sh
if the above command fails, then manually clone the repo and use the script scripts/get_june_data.sh.
Disclaimer: All the data is constructed by mixing different datasets from the Office for National Statistics (ONS), thus it may contain modifications. Please refere to the original source (cited in the release paper) for the raw dataset.
This will require a working installation of Openmpi or Intelmpi to compile mpi4py.
If you want to get the most up-to-date version of the code, then you can clone this repository, and install it using
pip install -e .
This should automatically install any requirements as well. You can then get the data using the same command as the pip version.
How to use the code
Have a look at Notebooks/quickstart.ipynb for a gentle introduction to how JUNE works. You can also checkout some scripts in example_scripts.
The docs directory contains the source files and HTML outputs to
display all information auto-generated from the june codebase docstrings,
including auto-generated class and module diagrams.
Tests
Run the tests with
cd test_june
pytest