covid19-vaccination-ch-qmd-pkg

The goal of covid19-vaccination-ch-qmd-pkg is to provide a Quarto dashboard article analyzing the weekly vaccination report from BAG (BundesAmt für Gesundheit - Swiss Federal Office for Public Health) collecting the data from the past 4 weeks.

The Vaccinated population is split into 3 categories:

• Fully Vaccinated with Booster
• Fully Vaccinated without Booster
• Partially Vaccinated

The categories above are compared with the Unvaccinated population.

Hospitalized and Deaths rates within the 4 populations are compared to analyze who is more at risk. The following measures are shown in the article:

• Hospitalization / Deaths counts
• Hospitalization / Deaths per 100'000 people

Entries with "Unknown" vaccination status are allocated to the 4 populations proportionally. Infection cases cannot be used for comparison because not provided by BAG.

The application fetches the data from BAG on a daily basis as part of a Continuous Integration / Deployment workflow. Given that BAG updates the data daily also for the past weeks (delay in communication) the presented results are also updated. A new week is published by BAG on Monday.

Package covid19vaccinationch

The covid19-vaccination-ch-qmd-pkg dashboard article is implemented through the supporting R package covid19vaccinationch that can be installed from GitHub with

remotes::install_github("miraisolutions/covid19-vaccination-ch-qmd-pkg")

and used to render the article locally from R via

# render
quarto::quarto_render("inst/report/index.qmd")
# run
quarto::quarto_run("inst/report/index.qmd")

# or
covid19vaccinationch::run_report()

See help file for using the latest data from BAG source.

Quarto article

The dashboard article is defined as an Quarto document inst/report/index.qmd shipped with the covid19vaccinationch package, containing the article text and the R code that reads and processes the data.

The Quarto document uses server: shiny and contains both ggplot2 / plotly graphs and shiny dynamic charts. The usage of server: shiny allows running the shiny chunks in the document.

Deployment to shinyapps.io

The covid19-vaccination-ch Quarto article is deployed to shinyapps.io and can be accessed at https://miraisolutions.shinyapps.io/covid19-vaccination-ch-qmd/.

Data building with GitHub Actions

It is likely that upon data structure changes from BAG the article might fail to render. For this reason, data are programmatically updated and checked as part of the Continuous Integration / Deployment GitHub Actions workflow .github/workflows/workflow.yml. The report will therefore show the latest working data until the package is update to be compatible with the new data structure.

Data are stored as RDS files inside the package under inst/bag_data, and used when rendering the article. A function of the package build_data() rebuilds the RDS files with the latest BAG data and overwrites them in inst/bag_data. This function is executed by the GitHub Action step "Fetch and rebuild latest BAG data" every Tuesday at 15:00 UTC (since April 2022 BAG switched to weekly updates, on Tuesdays at 15:30 Zurich time), and the updated data are tested (relying on R CMD check) and then committed and pushed to the main branch. Finally, the article with updated data is deployed to shinyapps.io, ensuring the application can be visualized with the daily updates.

BAG stopped updating data in September 2022. The automated data update of the app is interrupted.