Take a look at the discussion Best Practices for Organizing RMarkdown Projects, specifically this description of not doing everything in RMarkdown.
I have been using RMarkdown a little over a year. At first, I was so excited! I am not what you call an "A type personality" and it looked like .rmd would really help me keep all my data, code, and analysis together - another tool in my fight against my inherent chaos!
But the longer I worked on an analysis, the more my R notebook would become a complete and ugly monster. Scrolling, scrolling, scrolling. . .code, figures, text, tibbles, figures, code. . . I dreaded opening these things up. I quit R Notebooks and went back to scripts with labeled code chunks and comments. Then some one asked to see what I'm working on and I copied and pasted everything into .rmd and by this time my GitHub repo looks as bad as my kitchen counter.
So, if people who are here to argue for the use RMarkdown could at the same time provide more direction for best practices as intended, including some examples to emulate, this would go a longs ways into getting me back on the proper .rmd track.