Code for the paper "Using mobility data in the design of optimal lockdown strategies for the COVID-19 pandemic"

We report here code, data and results for France; inference is done with data until 31st August.

Content

The content of this repository is as follows:

• data contains the data used in the paper for model fit and optimal control. It contains both the raw data and the one formatted for using our code.
• plot_routines contains some scripts to produce plots in the paper.
• results contains the .jrl files used to store the inference results in the ABCpy library, together with some figures.
• src contains source code, with model definition and various utilities functions.
• Dataset_France.py is the Python script formatting the data before inference can be done.
• inference_SEI4RD_france_data.py is the script performing model fit; can be used with MPI parallelization by uncommenting one line.
• optimal_control_posterior_mean.py is the script performing optimal control under uncertainty, together with the definition of several functions to perform optimal control in specific cases.

Requirements

The following should install the required packages:

pip3 install -r requirements.txt

According to your python3 installation, you may require pip instead of pip3.