Add chapters and reorganize some of the content

[svteichman]

Purpose/implementation Section

This (draft) PR reorganizes some of the material, adding it into two new chapters for collecting and acquiring clinical data. The goal of this is to pull some of the material out of the data uses chapter, so that that chapter can really focus on how to use data (and not also include how to collect data).

What changes are being implemented in this Pull Request?

Two new chapters are added, "how to collect data" and "how to acquire data". They are added in that order after specific data types and before data uses.

Several sections that were previously in data uses are moved into the data collection chapter, including the sections on case report forms, clinical studies and trials, and research design considerations. Another section on observational studies (including different types of studies) is proposed.

The chapter about how to acquire data is mostly empty, with some proposed sections.

In the data uses chapter, the section on clinical data for cancer prevention and care is slightly reorganized to add subsections, and then content has been removed (and put into the data collection section). One question that I have here is in the section about questions that can be asked from retrospective analyses, if these questions actually apply to observational studies (both prospective and retrospective).

What was your approach?

I reorganized some of this material based on what I thought made for a more straightforward flow. This is a draft PR because this is my initial attempt but I want to get feedback before I move forward with this!

Tell potential reviewers what kind of feedback you are soliciting.

I am curious how this organization looks! Specifically,

• does adding chapters for collecting and acquiring data make sense?
• does the order in which I've added these chapters (with respect to the existing chapters) make sense?
• does separating out data collection from data uses make sense?
• it seems like we don't have content in the Google Drive (as far as I can tell) for acquiring data. Do these sections make sense and how should we go about drafting them?
• observation studies vs retrospective studies - how do we want to separate these out?
• do we want to add the additional sections that I've suggested/started to draft on specific types of observational studies (i.e. cohort studies, case-control studies, cross-sectional studies)?

New Content Checklist

• New content/chapter is in an Rmd file with this kind of format and headers.

• New content/chapter contains Learning Objectives and are in the correct format.

• Bookdown successfully re-renders and any new content files have been added to the _bookdown.yml.

• Spell check runs successfully in Github actions style-n-check).

• Any newly necessary packages that are needed have been added to the Dockerfile and image.

• Images are in the correct format for rendering.

• Every new image has alt text and is in a Google Slide.

• Each slide is described in the notes of the slide so learners relying on a screen reader can access the content. See https://lastcallmedia.com/blog/accessible-comics for more guidance on this.

• The color palette choices of the slide are contrasted in a way that is friendly to those with color vision deficiencies.
  You can check this using Color Oracle.

[github-actions]

No spelling errors! 🎉
Comment updated at 2026-07-07-17:45:41 with changes from 70e3b3f

[github-actions]

No broken url errors! 🎉
Comment updated at 2026-07-07-17:45:41 with changes from 70e3b3f

[github-actions]

Re-rendered previews from the latest commit:

• 👀 Quick preview of course website here *
• 🔬 Comprehensive download of the course website here
• Download the .docx file

* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.

Updated at 2026-07-07 with changes from the latest commit 70e3b3f