Day 8: Quarto, Part II

Recap from Day 7

• Quarto is a system for generating reports from code

• By using Quarto, we can ensure our results are reproducible and derived directly from the data (and code)

Due dates

• The report (report.qmd) is due 2025-07-30 11:59PM
  • Push your final commit to GitHub by the deadline
• The evaluation form is due 2025-08-06 11:59PM
  • Submit via Moodle

Grading

• Please see the rubric in the final report instructions to understand how the paper will be graded

• You will also evaluate each other’s final report using the rubric

  • I will post an anonymized version of each repository for you to evaluate and make an announcement on Moodle

How to evaluate the report

• Clone the repo as a new project and (try to) reproduce it by pressing the “render” button in RStudio
  • I will demonstrate with the example report (https://github.com/data-analysis-chiba/gapminder-report)
• You may need to edit the code to get it to render. Please try to do so.

How to evaluate the report

• Once you’ve reproduced the report, fill out the Final Report Evaluation form on Moodle

• Example Question: “Were you able to reproduce the code?”
  • 4: Yes, the code ran without any errors
  • 3: Yes, but only after making a very minor change myself, such as putting a file in a different folder
  • 2: Yes, but only after making several changes to the code
  • 1: No, even after trying to change it myself

• Example Question: “Which of the following best describes the introduction?””

  • 4: The dataset is described succinctly and clearly, including where it comes from.
  • 3: The overall purpose of the dataset is clear, but some details are lacking.
  • 2: Only the title of the dataset is given; no information about where the data come from.
  • 1: Introduction missing or no useful information provided

About .gitignore

Tell git to ignore output

• You should not commit the output of code
  • It clutters your git history, and is not necessary since you can always obtain the output by running the code

The .gitignore file

• If there are any files you don’t want git to track, you can ignore them by listing them in a special file called .gitignore.

• It is usually a good idea to ignore output files. We only want to track code (in other words, the analysis itself)

• You can tell git to ignore files by adding them to .gitignore:
  • gapminder-report.docx
  • gapminder-report.html
  • gapminder-report_files (files needed for HTML output)
• If you know you want to ignore all docx files, you could instead write this:
  • *.docx

Some tips for your report

Change the size of a figure

• You can adjust the size of the figure with chunk options fig.height and fig.width (units in inches)

• For example:

#| fig.height: 6
#| fig.width: 6

Change the font size

• You can adjust the overall font size of the figure like this:

ggplot(gapminder, aes(x = pop, y = lifeExp)) +
  geom_point() +
  theme_gray(base_size = 16)

Change the font size

• You can adjust the overall font size of the figure like this:

ggplot(gapminder, aes(x = pop, y = lifeExp)) +
  geom_point() +
  theme_gray(base_size = 16)

• There are other themes available too, but theme_gray() should be fine for the final paper

Add a pagebreak

• You can add a pagebreak to your document like this:

{{< pagebreak >}}

Final report

• The rest of the class time is to work on your final report. I will answer any questions you may have about the report.