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Temporal variation in transmission during the COVID-19 outbreak

This analysis has now be superseded. For the new results see here and see here and here for the supporting code.

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.

Usage

Set up

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:

Rscript utils/update_nowcasts.R

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.

Inspect results

Use 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.

Docker

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

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

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 tmp).

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

To access the command line run the following:

docker exec -ti covidglobalnow bash

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Temporal variation in transmission during the COVID-19 outbreak

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