Code for modelling estimated deaths and cases for COVID19.
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
All dependencies for the model can be provided by building a Docker image. Please note that using this method separate instructions are required to run the model - see details.
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.