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README.md
covid19model
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.
Installing dependencies
Using Conda
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
Using Docker
A Docker image providing all model dependencies is available. See docker/README.md for details of running the model with Docker.
Other
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.
How to run the code
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.