COVID-19-Publication-Dashboard

Dashboard for weekly COVID-19 publication

Since the start of the COVID-19 outbreak Public Health Scotland (PHS) has been working closely with Scottish Government and health and care colleagues in supporting the surveillance and monitoring of COVID-19 amongst the population.

Each week, a statistical report covering COVID-19 in Scotland is published. This report can be found here.

This GitHub repository contains the R project for the accompanying interactive shiny dashboard.

Workflow

Data transfer

• The necessary data will be assembled in the weekly report data folder each week on a Monday/Tuesday
• Copy the data to /conf/C19_Test_and_Protect/Test & Protect - Warehouse/Weekly Dashboard Data/Input/
• Check you have the latest (or appropriate) version of this repository
• Run dashboard data transfer by sourcing the script and interacting with R Studio as necessary to select the correct files

App preparation

• Obtain uncommitted files from colleagues shiny_app/www/google-analytics.html and shiny_app/AppDeployment.R
• Update paths in AppDeployment.R so that they match where your dashboard copy is located
• Run app_data_preparation.R to transfer the processed data to your shiny_app/data folder as .rds files
• Go to global.R and change the report date to this week's report date
• Run global.R and check through the app

App deployment

• Go to AppDeployment.R and run file (run first section only for PRA deployment)

Development

Code layout

• app_data_preparation.R is a script for copying .csv files from shared filepath to local shiny_app/data/ folder
• Dashboard Data Transfer contains the files for processing data for the app. The process is orchestrated from dashboard_data_transfer.R, which successively runs the scripts inside Dashboard Data Transfer/Transfer scripts.
• shiny_app contains the code for the app.
  • ui.R, server.R and global.R are the primary app scripts
  • www contains the css stylesheet and PHS logo and favicon
  • functions contains functions for the app
    • functions_tables.R contains functions for tables
    • functions_chart_layout.R contains functions for organising charts and titles
    • functions_server.R contains other functions including those for graphs
  • tabs contains R files with content for each of the tabs