I too prefer RStudio/RMarkdown. Now we have the Reticulate package that allows running Python inside RMarkdown, for my purposes it's way better than Jupyter. It

I too prefer RStudio/RMarkdown. Now we have the Reticulate package that allows running Python inside RMarkdown, for my purposes it's way better than Jupyter. It's just plain text so my editor and VCS and everything plays nicely. But perhaps the biggest strength is that you go through Pandoc, so you can just click a button and get the output as a Word file for sending to someone who's not a software dev, or you can get it as a LaTeX source file and extend it into a proper formal document like a journal paper, or you can do it as HTML where embedding Bokeh scripts and other interactive things Just Works. I've even made presentations with it going through the reveal.js framework, where you can put an interactive plot on one of your slides, and show people live "what happens when we change this parameter". That's still semi-witchcraft in 2018, but it's going to become a common thing (hopefully).