⭐⭐⭐ Parametrise your report

This exercise builds on the previous exercises where you learnt to create a simple MS Word report ⭐ and to add dynamic elements to your report ⭐⭐. Mastering these two exercises is essential for successfully completing the current exercise.

1 Objectives 🎯

• If you have generated the MS Word report with dynamic elements as instructed in Exercise 4, continue working on the same Quarto notebook you already modified. Otherwise, download the files df1.RData, df2.RData, exercise5.qmd, swisstph_template.docx, and my_biblio.bib using the links provided on the right-hand side of this page. For simplicity, please put these two files under the same folder and open the Quarto notebook in RStudio.
• Complete each of the following tasks and render the document after each task or set of tasks to track your progress.

2 Use Quarto in a terminal

• Render your MS Word report using the RStudio Terminal;

quarto render exercise5.qmd

• Change the output filename when rendering the report;

quarto render exercise5.qmd -o exercise5_report1.docx

Tip

• You can access the RStudio terminal in the Terminal tab immediately to the right of the Console tab:

• If the terminal tab is not visible, go to Tools > Terminal > Move Focus to Terminal

3 Parametrise your report

• Adjust the report to focus on data for the year 2022 only ;
• You were unfortunately provided with a previous erroneous version of the dataset. Update the report to use the dataset stored in df2.RData instead of the one stored in df1.RData ;
• Render 3 reports (1 report with df2.RData for the full outbreak period, 1 report with df1.RData for year 2021 only, 1 report with df2.RData for year 2021 only) adapting the following command which needs to be run in a terminal (ensure your working directory is the one where your Quarto document is stored and all file paths are correct).
• Create a small R script using purrr::walk() or a for loop that calls quarto::quarto_render() to generate 5 separate reports automatically.
• How would you ensure that the report doesn’t ‘break’ if a user inputs a year that does not exist in the data? How would you implement a ‘sanity check’ code chunk?

quarto render exercise5.qmd -o exercise5_report_df1.docx -P dataset:df1.RData

Tip

• See Quarto documentation about parameters
• See Quarto documentation about rendering outputs using different parameters

ImportantDiscussion question

Discuss the advantages and disadvantages of using R within Quarto compared to using R scripts.