The notes themselves are created using LaTeX, R, and knitr using a LaTeX style I created that is a compromise format between projecting slides and printing notes. In the future I will explore using bookdown for creating content in html instead of pdf. In either case, the notes can change significantly when R commands within them are re-executed by knitr in R.
An example of a page of pdf notes with icons that link to audio or video content is in Section 10.5 of BBR. I add red letters in the right margin for each subsection in the text, and occasionally call out these letters in the audio so that the student will know where I am.
There are several student activities for which the course would benefit by recording information. Two of them are students pooling notes taken during class sessions, and questions and answers between sessions. The former might be handled by simultaneous editing or wiki curation on the cloud, and I haven't thought very much about how to link this with the course notes to in effect expand the notes for the next class of students. Let's consider the Q&A aspect. It would be advantageous for questions and answers to "grow", and for future students to take advantage of the Q&As from past students. Being able to be looking at a subsection in the course notes and quickly linking to cumulative Q&A on that topic is a plus. My first attempt at this was to set up a slack.com team for courses in our department, and then setting up a channel for each of the two courses I teach. As slack does not allow sub-channels, the discussions need to be organized in some way. I went about this by assigning a mnemonic in the course notes that should be mentioned when a threaded discussion is started in slack. Students can search for discussions about a subsection in the notes by searching for that mnemonic. I have put hyperlinks from the notes to a slack search expression that is supposed to bring up discussions related to the mnemonic in the course's slack channel. The problem is that slack doesn't have a formal URL construction that guarantees that a hyperlink to a URL with that expression will cause the correct discussions to pop up in the user's browser. This is a work in progress, and other ideas are welcomed. See Section 10.5.1 of BBR for an example where an icon links to slack (see the mnemonic reg-simple).
Besides being hard to figure out how to create URLs o get the student and instructor directly into a specific discussion, slack has the disadvantage that users need to be invited to join the team. If every team member is to be from the instructor's university, you can configure slack so that anyone with an email address in the instructor's domain can be added to the team automatically.
I have entertained another approach of using disqus for linking student comments to sections of notes. This is very easy to set up, but when one wants to have a separate discussion about each notes subsection, I haven't figured out how to have disqus use keywords or some other means to separate the discussions.
stats.stackexchange.com is the world's most active Q&A and discussion board for statistics. Its ability to format questions, answers, comments, math equations, and images is unsurpassed. Perhaps every discussion about a statistical issue should be started in stackexchange and then linked to from the course notes. This has the disadvantage of needing to link to multiple existing stackexchange questions related to one topic, but has the great advantage of gathering input from statisticians around the world, not just those in the class.
No mater which method for entering Q & A is used, I think that such comments need to be maintained separately from the course notes because of the dynamic, reproducible nature of the notes using knitr. Just as important, when I add new static content to the notes I want the existing student comments to just move appropriately with these changes. Hyperlinking to Q & A does that. There is one more issue not discussed above - students often annotate the pdf file, but their annotations are undone when I produce an update to he notes. It would be nice to have some sort of dynamic annotation capability. This is likely to work better as I use R bookdown for new notes I develop.
I need your help in refining the approach or discovering completely new approaches to coordination of information using the course notes as a hub. Please add comments to this post below, or short suggestions to @f2harrell on twitter.