mherreshoff / c19map

Import script and models for the c19map.org project

c19map.org scripts

This repository contains scripts to help run the c19map.org project.

• import.py - Pulls data from John's Hopkins University and from our spreadsheet with intervention and population data and outputs some files.
• predict.py - Runs our model on that data and outputs some prediction CSV files, and graphs.

Setup

In order to run predict.py we first need to compile the integrator for our differential equation, using the following commands:

./compile_integrators.py
python3 setup.py build_ext --inplace

The first command generates the integrators.pyx file which can integrate the differential equation for our model (and can also optionally calculate a sensitivity matrix for use with differential methods.) The second command compiles integrators.pyx into a fast library we can import.