COVIDScenarioPipeline
Public shared code for doing scenario forecasting and creating reports for various governmental entities.
Howto
Set up the repository
Please see the Wiki for this repository for updated instructions on how to clone the repository and push/pull changes.
If making changes to this repository, please do it directly instead of through the submodule of another repository.
Run the code
After cloning the repository (see Wiki for instructions on how to clone a repository with submodules) create setup in a subfolder of the data using the notebook data/build-model-input.ipynb. This creates two files:
mobility.txt: mobility matrix from us commute, as in An Economic Geography of the United States: From Commutes to Megaregions by Garrett Dash Nelson and Alasdair Rae processed by Ed King on Kagglegeodata.csv: specification of the spatial nodes, with at least column for the index, the geoid or name, the population.
Then copy the main_template.py from this repo into the root of the SPATIAL_SETUP_REPO folder. Changes the first line and you're ready to run it.
if you haven't installed python packages, run
pip3 install pandas numpy seaborn matplotlib geopy tqdm geopandas shapely numba rpy2
You can now run the code:
nohup python3 main.py > out.txt &
creates a figure/ and a SCENARIO_model_output_TIMESTAMP folder.