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.
Aim: To identify changes in the reproduction number, rate of spread, and doubling time during the course of the COVID-19 outbreak whilst accounting for potential biases due to delays in case reporting.
Set your working directory to the home directory of this project (or use the provided Rstudio project). Install the analysis and all dependencies with:
remotes::install_github("cmmid/CovidGlobalNow", dependencies = TRUE)
Update all regional nowcasts and report
All regional nowcasts and the report can be updated by running the following from the package root directory:
Update individual nowcasts
Individual nowcasts can be updated (and their assumptions inspected) in the
nowcasts folder. Nowcasts are labelled as
region_nowcast.R. Results from each nowcast are stored in
results/region/nowcast_date. It is assumed that the user is in the project root for all analysis.
vignettes/global-report.Rmd to inspect the results of the analysis interactively. See
vignettes/global-report.md for a markdown version of the analysis containing all results. See
vignettes/rendered_output for version of the analysis rendered in other formats.
This analysis was developed in a docker container based on the
rocker/geospatial docker image.
To build the docker image run (from the
docker build . -t covidglobalnow
To run the docker image run:
docker run -d -p 8787:8787 --name covidglobalnow -e USER=covidglobalnow -e PASSWORD=covidglobalnow covidglobalnow
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
covidglobalnow directory to
To access the command line run the following:
docker exec -ti covidglobalnow bash