In the mid-90s I was a Mech Eng undergrad using a program called MathCAD which provided a "notebook" interactive computation mixed with text environment by running as a Word plugin. In 2018 I use Jupyter and it's not clear where the progress has been. There are too many compromises trying to make it work in a web browser. For what Jupyter is for I find that RStudio or Spyder are infinitely superior. I do interactive exploring and transforming that into both documents and reusable and deployable code all in the one tool
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).
One has to strecth the term quite a lot to say that RStudio is a "native" GUI. The interface is just a browser window, the only native part is the menu bar.
