Warning: This package is a work in progress and is currently developed solely with the COVID-19 outbreak in mind. Breaking changes may occur and the authors cannot guarantee support.
Aim: To identify changes in the reproduction number, rate of spread, and doubling time during the course of outbreaks whilst accounting for potential biases due to delays in case reporting.
Install the analysis and all dependencies with:
remotes::install_github("epiforecasts/EpiNow", dependencies = TRUE)This package was developed in a docker container based on the rocker/geospatial docker image.
To build the docker image run (from the EpiNow directory):
docker build . -t epinowTo run the docker image run:
docker run -d -p 8787:8787 --name epinow -e USER=epinow -e PASSWORD=epinow time_varyThe rstudio client can be found on port :8787 at your local machines ip. The default username:password is epinow:epinow, 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 epinow directory to tmp).
--mount type=bind,source=$(pwd)/tmp,target=/home/time_vary
To access the command line run the following:
docker exec -ti epinow bash