Code for modelling estimated deaths and cases for COVID19 from Report 13 published by MRC Centre for Global Infectious Disease Analysis, Imperial College London: Estimating the number of infections and the impact of nonpharmaceutical interventions on COVID-19 in 11 European countries

This repository has code for replication purposes. The bleeding edge code and advancements are done in a private repository. Ask report authors for any collaborations.

An environment.yml file is provided and can be used to build a virtual environment containing all model dependencies. Create the environment using:

conda env create -f environment.yml

Then activate the environment for use:

conda activate covid19model

A Docker image providing all model dependencies is available. See docker/README.md for details of running the model with Docker.

If you wish to install packages into your native R environment or with a system package manager please see environment.yml for a full list of dependencies.

There are two ways to run our code:-

• Open the rstudio project covid19model.Rproj file in rstudio and run/source base.r file
• To run from commandline please enter the cloned directory and type 'Rscript base.r base' in terminal
• The results are stored in two folders results and figures.
• Results has the stored stan fits and data used for plotting
• Figures have the images with daily cases, daily death and Rt for all countries.