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 England; inference is done with data until 23rd May and 31st August.
The preprint which focuses on England can be found at:
https://arxiv.org/pdf/2006.16059.pdf
Please also check the companion website, where updates on subsequent research will be described:
https://optimallockdown.github.io/Covid19inEngland/
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.Datasets.ipynb
is a jupyter notebook exemplifying the data sources and the data processing operations before fitting the model, for inference with observed data until 23rd May.Dataset_England.py
is instead a Python script used to format data for inference with observations until 31st August.inference_SEI4RD_england_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.
The following should install the required packages:
pip3 install -r requirements.txt
According to your python3 installation, you may require pip
instead of pip3
.