Code associated with the paper: Heterogeneous transmission in groups induces a superlinear force of infection
The scripts make use of 3 different submodules:
- hgcm for the approximate master equations framework
- horgg for the synthetic generation of hypergraphs
- schon for the simulation of contagions on hypergraphs Please refer to each submodule for their own requirements.
We also make use of standard python packages numpy, scipy, matplotlib,
and many others. See the requirement.txt file.
First clone the repository and the submodules using
git clone --recurse-submodules git@github.com:gstonge/heterogeneous-transmission.git
or
git clone --recurse-submodules https://github.com/gstonge/heterogeneous-transmission.git
We suggest to start a new python virtual environment and install all requirements using
pip install -r requirements.txt
Depending on the modules you want to use, you might need to install hgcm, horgg, and/or schon.
Please refer to each submodule installation instructions.
The following command should work if the requirements were installed properly:
pip install hgcm horgg schon
Each jupyter notebook that create the figures need some data to be generated. Go to the appropriate directory and follow instructions.