[R] RMarkdown vignettes v. Jupyter notebooks?

[Ista Zahn]

On Thu, Oct 11, 2018 at 10:15 AM Yihui Xie <xie using yihui.name> wrote:
>
> I just have one comment on the multi-language support in R Markdown
> (inline below):
>
> On Thu, Oct 11, 2018 at 6:19 AM Ista Zahn <istazahn using gmail.com> wrote:
> >
> > Hi Spencer,
> >
> > On Thu, Oct 11, 2018 at 5:08 AM Spencer Graves
> > <spencer.graves using effectivedefense.org> wrote:
> > >
> > > Hello:
> > >
> > >
> > >        What are the differences between Jupyter notebooks and RMarkdown
> > > vignettes?
> >
> > Here are some of the main differences I'm aware of:
> >

<snip>

> > Rmarkdown is specific to R (I guess there is some basic support in
> > knitr for other languages, but in my experience it never worked well)
> > while Jupyter notebooks are language agnostic and "kernels" exist for
> > a large number of programming languages. However, each Jupyter
> > notebook can use only one kernel; you can't easily have R and Python
> > code in the same notebook.
>
> You might want to at least update your impression about the Python
> support in R Markdown now :) Last year, with the release of the
> reticulate package, the support for Python has been substantially
> enhanced in both R Markdown
> (https://bookdown.org/yihui/rmarkdown/language-engines.html) and
> RStudio (https://blog.rstudio.com/2018/10/09/rstudio-1-2-preview-reticulated-python/).
> You can easily have both R and Python code in the same R Markdown
> document, and the two worlds can freely talk to each other.

Yes, I did miss that development, thank you for that! I haven't spent
much time with it yet, but that looks really great.

--Ista
>
> > Jupyter notebooks typically run in your browser where the actual text
> > editing features are somewhat limited. Rmarkdown is typically run in
> > an editor such as Emacs or Rstudio where editing and project support
> > is much better and greater customization may be possible. You can work
> > indirectly with Jupyter notebooks in Emacs
> > (https://github.com/millejoh/emacs-ipython-notebook) and perhaps other
> > editors as well; this goes some way toward escaping the tyranny of the
> > browser but is more fragile and difficult to get working compared to
> > Rmarkdown.
> >
> > Because Jupyter uses a web-based client-server model, it is easy to
> > provide live interactive notebooks on your website (see e.g.,
> > https://github.com/jupyterhub/binderhub). As far as I know this is not
> > currently possible with Rmarkdown.
> >
> > >
> > >
> > >        I'm trying to do real time monitoring of the broadcast quality of
> > > a radio station, and it seems to me that it may be easier to do that in
> > > Python than in R.[1]  This led me to a recent post to
> > > "python-list using python.org" that mentioned "Jupyter, Mathematica, and the
> > > Future of the Research Paper"[2] by Paul Romer, who won the 2018 Nobel
> > > Memorial Prize in Economics only a few days ago.  In brief, this article
> > > suggests that Jupyter notebooks may replace publication in refereed
> > > scientific journals as the primary vehicle for sharing scientific
> > > research, because they make it so easy for readers to follow both the
> > > scientific and computational logic and test their own modifications.
> > >
> > >
> > >        A "Jupyter Notebook Tutorial: The Definitive Guide"[3] suggested
> > > I first install Anaconda Navigator.  I got version 1.9.2 of that.  It
> > > opens with options for eight different "applications" including
> > > JupyterLab 0.34.9, Jupyter Notebook 5.6.0, Spyder 3.3.1 (an IDE for
> > > Python), and RStudio 1.1.456.
> > >
> > >
> > >        This leads to several questions:
> > >
> > >
> > >              1.  In general, what experiences have people had with
> > > Jupyter Notebooks, Anaconda Navigator, and RMarkdown vignettes in
> > > RStudio, and the similarities and differences?  Do you know any
> > > references that discuss this?
> >
> > I've used both extensively, and noted the differences I've discovered above.
> >
> > >
> > >
> > >              2.  More specifically, does it make sense to try to use
> > > RStudio from within Anaconda Navigator, or is one better off using
> > > RStudio as a separate, stand alone application -- or should one even
> > > abandon RStudio and run R instead from within a Jupyter Notebook? [I'm
> > > new to this topic, so it's possible that this question doesn't even make
> > > sense.]
> >
> > The only advantage I can think of to using Rstudio via Anaconda is
> > that you could use conda environments to maintain different versions
> > or R and/or R packages for different projects.
> >
> > You'll have to weigh the pros and cons to decide whether to switch
> > from Rstudio to Jupyter notebooks. Depending on what you want to do
> > there are both advantages and disadvantages, as discussed above.
> >
> > Finally, I have to give a plug for a couple of related tools that I
> > find very useful.
> >
> > Emacs org-mode https://orgmode.org/ gives you the best of both worlds:
> > notebooks unconstrained by the browser that can include code in
> > multiple languages, header arguments, excellent export support, etc.
> > It is superior to both Jupyter and Rmarkdown, except that support only
> > exists in Emacs.
> >
> > Jupytext (https://github.com/mwouts/jupytext) is another way to have
> > it all, by allowing you to edit in markdown or Rmarkdown, and
> > auto-generating a notebook and possibly other formats for you. I've
> > only recently started experimenting with it, but so far I like it a
> > lot.
> >
> > Best,
> > Ista
> > >
> > >
> > >        Thanks,
> > >        Spencer Graves
> > >
> > >
> > > [1] If you have ideas for how best to do real time monitoring of
> > > broadcast quality of a radio station, I'd love to hear them.  I need
> > > software that will do that, preferably something that's free, open
> > > source.  The commercial software I've seen for this is not adequate for
> > > my purposes, so I'm trying to write my own.  I have a sample script in
> > > Python that will read a live stream from a radio tuner and output a
> > > *.wav of whatever length I want, and I wrote Python eight years ago for
> > > a similar real time application.  I'd prefer to use R, but I don't know
> > > how to get started.
> > >
> > >
> > > [2] 2018-04-13:
> > > "https://paulromer.net/jupyter-mathematica-and-the-future-of-the-research-paper".
> > > This further cites a similar article in The Atlantic from 2018-04-05:
> > > "www.theatlantic.com/science/archive/2018/04/the-scientific-paper-is-obsolete/556676".