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.