What are the advantages of writing a thesis with rMarkdown? I think the question is self-explanatory but to add a bit of a background, I'll be starting my M.Sc. research quite soon and I want to create and maintain a workflow that allows me to devote my time to doing exploratory and inferential analysis, devoting my time to pondering on results, and assuring reproducibility. 

With word processing tools like Microsoft Word, I fear I'd spend a great share of time focusing on editing and layout.

With that said, I'd like to know about your experience - bad or good - using rMarkdown to write your thesis? What were the advantages you felt by this choice, and what were the things that slowed you down? 

In case you used an alternative "language" and are willing to share your reasons about your choice and how it went for you, please, go ahead.
RMarkdown allows you to put your code directly into you manuscript and is functionally an easier to use replacement for Sweave. 

The same advantages and disadvantages listed in this previous answer hold for RMarkdown as well. 

Last, Chester Ismay has created a thesisdown template, which would be a good starting place for you.