Tools for forecasting COVID-19 Propagation at the US County Level. We implement a generalized comparmental model based on the SEIR formalism.
The top figure represents unsupressed COVID19 flow through the population, while the second figure demonstrates the impact of distancing policies.
Install miniconda python 3.7 from here https://docs.conda.io/en/latest/miniconda.html
Execute
conda env create -f environment.yaml
Activate the environment here..
conda activate pyseir
Change to into the county_covid_seir_models directory
pip install -e .
pyseir run-all --state=California
This will take a few minutes to download today's data, run inference and model
ensembles, and generate the output. Then check the output/
folder for results.
###4/3
- Add hospital admissions per day
- Add deaths per day
- Compute surge window start/end
- Plots case data and death data to county specific reports (still not yet fitting to death data: coming soon)
- Add empirical suppression policiesProduce 0%, 25%, 50%, 65% mitigation projections
- Reduce hospitalizations infection from 20% -> 10%