So I normally use R-Notebook and I didn't know about Markdown. I'm not going to change over to Markdown. But I just learned that knitting to an HTML from Markdown doesn't let you create an HTML like R-Notebook's.
R-Notebook automatically creates an HTML and in the upper right hand corner there's a drop down that allows the you to either "Show All Code" or "Hide All Code" as well as "rmd Download". When I was originally taught in R, my professor said R Notebooks are meant for sharing your code. So we never used anything else but R Notebook--and I still haven't changed that habit.
The downloadable part is the important part because my group and I just found out that while my HTMLs from Notebook are downloadable as R files, the knitted HTML files from Markdown does not have the downloadable option like mine do. This is not a huge problem because we can send both the HTML and R files back and forth.
But it would be good to know if there is a way to create an HTML from Markdown that is rmd downloadable, the way R Notebook allows them to download my files.