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/
• The data underlying the app can be found on the PHS open data website (external link)

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), although file names can differ. Contact phs.covid19data&analytics@phs.scot 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.