covid19uk

Files

• covid Python package

  • model.py main CovidUKODE model class
  • rdata.py functions to import R .rds files with data
  • pydata.py functions for importing files not from R .rds files
  • util.py utility functions

• covid_ode.py script that runs a test simulator

• mcmc.py fits the model

• prediction.py ingests a posterior from mcmc.py, calculates predictions (saved in pred_2020-03-15.h5) file.

• ode_config.yaml default YAML configuration file for Covid-19 model (used by the 3 files above)

• household_sim.py experimental (and probably broken) code

• environment.yaml conda description of the required environment. Create with conda create --file environment.yaml