Temporal variation in transmission during the COVID-19 outbreak

Warning: This analysis is a work in progress. Breaking changes may occur and the authors cannot guarantee support.

Usage

Clone the website

This repository uses submodules to store results. To download these at the same time as cloning the main repository use the following:

git clone --recursive https://github.com/epiforecasts/covid.git

Update external results

Update all external results using the following git call.

git submodule update --init --recursive

Update the website

Update

Update all nowcasts and deploy the website with the following:

bash bin/update_website.sh

Docker

This analysis was developed in a docker container based on the rocker/geospatial docker image.

To build the docker image run (from the covid directory):

docker build . -t covid

To run the docker image run:

docker run -d -p 8787:8787 --name covid -e USER=covid -e PASSWORD=covid covid

The RStudio client can be found on port :8787 at your local machines ip. The default username:password is time_vary:time_vary, set the user with -e USER=username, and the password with - e PASSWORD=newpasswordhere. The default is to save the analysis files into the user directory.

To mount a folder (from your current working directory - here assumed to be tmp) in the docker container to your local system use the following in the above docker run command (as given mounts the whole covid directory to tmp).

--mount type=bind,source=$(pwd)/tmp,target=/home/covid

To access the command line run the following:

docker exec -ti covid bash