https://github.com/epiforecasts/covid
Temporal variation in transmission during the COVID-19 outbreak
https://github.com/epiforecasts/covid
covid
Last synced: 3 months ago
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Temporal variation in transmission during the COVID-19 outbreak
- Host: GitHub
- URL: https://github.com/epiforecasts/covid
- Owner: epiforecasts
- License: mit
- Created: 2020-03-21T15:44:20.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2022-05-18T08:44:54.000Z (over 3 years ago)
- Last Synced: 2025-06-14T13:06:01.450Z (4 months ago)
- Topics: covid
- Language: TeX
- Homepage: https://epiforecasts.io/covid/
- Size: 11.5 GB
- Stars: 109
- Watchers: 14
- Forks: 30
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Temporal variation in transmission during the COVID-19 outbreak
For the underlying estimates see [here](https://github.com/epiforecasts/covid-rt-estimates). See [here](https://github.com/epiforecasts/EpiNow2) for documentation on the methodology used. See [here](https://github.com/epiforecasts/covidregionaldata) for our data back-end.
## Usage
### Clone the website
```bash
git clone --depth 1 https://github.com/epiforecasts/covid.git
```
### Update results
This repository uses Azure blob storage to store results. To download these first install [`azcopy`](https://docs.microsoft.com/en-us/azure/storage/common/storage-use-azcopy-v10) (see here for a script to do this for [Linux](https://github.com/epiforecasts/covid-rt-estimates/blob/master/bin/install_azcopy.sh)) and then run the following.
```bash
Rscript utils/update_estimates.R
```
*Warning when run for the first time this will download several GB of data. See [`covid-rt-estimates`](https://github.com/epiforecasts/covid-rt-estimates) for further support accessing estimates.*
### Update the website
#### Update
Update the website with the following:
```bash
bash bin/update_website.sh
```
See the `bin` folder for other updating scripts.
## 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):
```bash
docker build . -t covid
```
To run the docker image run:
```bash
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`).
```{bash, eval = FALSE}
--mount type=bind,source=$(pwd)/tmp,target=/home/covid
```
To access the command line run the following:
```{bash, eval = FALSE}
docker exec -ti covid bash
```