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README.md
Contributing
This project welcomes contributions and suggestions. Most contributions require you to agree to a Contributor License Agreement (CLA) declaring that you have the right to, and actually do, grant us the rights to use your contribution. For details, visit https://cla.opensource.microsoft.com.
When you submit a pull request, a CLA bot will automatically determine whether you need to provide a CLA and decorate the PR appropriately (e.g., status check, comment). Simply follow the instructions provided by the bot. You will only need to do this once across all repos using our CLA.
This project has adopted the Microsoft Open Source Code of Conduct. For more information see the Code of Conduct FAQ or contact opencode@microsoft.com with any additional questions or comments.
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.
Contributing
We welcome all potential collaborators and contributors from the wider community. Please see contributing for more details.
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.