https://github.com/public-health-scotland/covid-19_respiratory_surveillance_dashboard
A Public Health Scotland R shiny app for surveillance of COVID-19 and respiratory illnesses in Scotland
https://github.com/public-health-scotland/covid-19_respiratory_surveillance_dashboard
app covid-19 dashboard public-health respiratory scotland shiny surveillance
Last synced: 22 days ago
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A Public Health Scotland R shiny app for surveillance of COVID-19 and respiratory illnesses in Scotland
- Host: GitHub
- URL: https://github.com/public-health-scotland/covid-19_respiratory_surveillance_dashboard
- Owner: Public-Health-Scotland
- Created: 2023-02-01T13:17:38.000Z (over 2 years ago)
- Default Branch: new_structure_cm
- Last Pushed: 2024-11-06T13:56:23.000Z (6 months ago)
- Last Synced: 2024-11-06T14:43:55.707Z (6 months ago)
- Topics: app, covid-19, dashboard, public-health, respiratory, scotland, shiny, surveillance
- Language: R
- Homepage: https://scotland.shinyapps.io/phs-respiratory-covid-19/
- Size: 15 MB
- Stars: 4
- Watchers: 2
- Forks: 0
- Open Issues: 3
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Metadata Files:
- Readme: README.md
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README
# COVID-19 and Respiratory Surveillance in Scotland
* This is a Public Health Scotland R shiny app available to the public at [https://scotland.shinyapps.io/phs-respiratory-covid-19/](https://scotland.shinyapps.io/phs-respiratory-covid-19/)
* The data underlying the app can be found on the [PHS open data website (external link)](https://www.opendata.nhs.scot/)
## Additional files needed to run the R shiny app
* Various data files are required which can be found on [PHS open data website (external link)](https://www.opendata.nhs.scot/), although file names can differ. Contact [phs.covid19data&[email protected]](mailto:phs.covid19data&[email protected]) for further information
* The following files must be obtained from colleagues:
* `shiny_app/www/google-analytics.html`
* `shiny_app/deployment/deployment_secrets.R`
* `shiny_app/password_protect/credentials.rds`
## Deploying the R shiny app
1. Navigate to `Dashboard Data Transfer/dashboard_data_transfer.R` and source. This prepares the data for use in the app.
2. Run `app_data_preparation.R` to transfer the prepared files to `shiny_app/data`.
3. Run app from `shiny_app/app.R` to view app locally to check content.
4. Obtain `shiny_app/deployment/deployment_secrets.R` from colleagues. Edit the paths to point to your local `shiny_app` folder.
5. Go to `shiny_app/deployment/deploy_app.R` and set the `pra` flag to TRUE for deployment to password protected pre-release access site or FALSE for deployment to public site.
6. Source the script to deploy the app.
## Developing the R shiny app
### Data transfer layout
* `Dashboard Data Transfer` contains the data transfer code. This is for transferring data from mixed inputs to open data format ready for use in the app.
* `dashboard_data_transfer.R` is the script for doing the transfer
* `Transfer Scripts` contains individual scripts called from `dashboard_data_transfer.R`
### App code layout
* `shiny_app` contains all the app code
* `app.R` is the main app file
* `setup.R` contains the necessary packages and some settings. This is run once on deployment and not for every new user. It also loads all the data in `shiny_app/data`.
* `data` contains all the data needed for the shiny app. It is populated using the `app_data_preparation.R` script
* `functions` contains general functions used in several places across the app.
* `core_functions.R` includes general functions and also functions for making data tables
* `plot_functions.R` includes general plotting functions
* `www` contains static images as well as additional css and javascript code
* `deployment` contains code for deploying the app to shinyapps.io
* `modules` contains sub-folders of shiny modules used by the app
* `indicators` contains sub-folders for each topic/tab in the app. Each sub-folder contains a ui script, a server script and a functions script.