EpiGeoPop

This repository is a snakemake workflow for getting population density data for arbitrary countries. It uses population data from the JRC Big Data Analytics Platform, border data from Natural Earth, and is partially based on Adam Symington's excellent blog post. This workflow is motivated by extending epiabm to other countries.

The workflow generates population density files that look like:

and can generate figures of simulations like:

or animations like:

Running

The following shows how to setup and run the Snakemake pipeline. By default, it will create the files for running a Luxembourg simulation, but the Snakefile can be modified to generated files for many countries, province/states, or cities.

Clone the repository

git clone [email protected]:SABS-R3-Epidemiology/EpiGeoPop.git
cd EpiGeoPop

Create virtual environment (recommended)

python -m venv venv
source venv/bin/activate

Install dependencies

pip install -r requirements.txt

Downlaod the raw data (See data/README.md for more information)

bash prep.sh

Run the snakemake pipeline

snakemake --cores 1

Exploring the data

Check the outputs directory for example population density maps. The image outputs/dag.svg shows the entire workflow. The file data/processed/countries/Luxembourg_microcells.csv contains the generated microcells, used for input to simulations such as epiabm. The file data/processed/countries/Luxembourg_pop_dist.json contains the age distribution of populations.

Running on other regions

The Snakefile contains commented out examples of other regions to show how to generate files for other countries, provinces, and cities. These also require a configuration file which can be copied from similar files in the configs directory.

Generating animations

The file make_gif.py in data/sim_outputs is used for making GIFs and grids from simulation input data. To use it, add the simulation output file to data/sim_outputs, edit the filename in make_gif.py, and run python make_gif.py. The resulating animation and grid of time snapshots will be stored in data/sim_outputs/animation. An example on Winnipeg (Canada) is provided in this repository.