Looking for good practice/workflow for drafting thesis and manuscripts using bookdown

Hello. I'm a PhD student and I was considering whether I should use bookdown to prepare my thesis and manuscripts. I've read through Yihui's book Authoring Books with R Markdown and several other guidance, basically figuring out the usage of it. However, I still have some concern:

  1. How to collaborate with my supervisor working on the word document?
    I've read some people's experiences that we can manually incorporate the supervisor's changes into .Rmd file. But when we regenerate the word document, the labels and comments made by the supervisor wouldn't exist anymore. Could the supervisor happy with it? Is there any other practice/workflow around it?

  2. When we encountered a complicated table, is it easy to generate?

  3. How about the final typesetting?
    For word, after knitting the .Rmd file, perhaps I have to tweak something in the final word document, such as resize big figure or modify table format. And for pdf, I'm not familiar with latex and I still need to look at how to control the final appearance in the pdf format.

In general, I know bookdown is a perfect tool to prepare the online book or teaching materials, but I'm not sure how to use it properly when preparing the thesis and manuscripts. Therefore, I hope to hear your advice.

Many thanks for your guidance and all the best to your health.

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It will not directly answer your question but if you did not look at them yet, you should see the different examples submitted during bookdown contest. There were a few thesis, which some that won a prize

See the bookdown page about those:

And the contest category here

hope it helps

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Thank you very much @cderv. These materials are really helpful and interesting. I'll look it through and have a try.