[R] RMarkdown vignettes v. Jupyter notebooks?

Ista Zahn |@t@z@hn @end|ng |rom gm@||@com
Thu Oct 11 14:53:29 CEST 2018 

On Thu, Oct 11, 2018 at 8:36 AM Duncan Murdoch <murdoch.duncan using gmail.com> wrote:
>
> On 11/10/2018 7:18 AM, Ista Zahn 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:
> >
> > Rmarkdown files include code and prose. The results produced by the
> > code do not appear in the Rmarkdown file; instead, the file must be
> > processed and typeset to produce a .pdf or .html (etc.) file that
> > includes those results. Jupyter notebooks dispense with with
> > processing step: output is displayed directly in the notebook. That
> > is, a notebook includes code, prose, and results, while an Rmarkdown
> > file includes only code and prose.
>
> RStudio can display the output mixed in with the text in the editor.

True, but the _file_ does not include the output. Thus it functions
more as a preview, and will not be visible to you if I email you a
.Rmd file. On the other hand, .ipynb files really do contain the
output; if I email one to you and you open it in Jupyter you will see
the output as well.

--Ista

>
> >
> > Rmarkdown allows control over the inclusion of code and results, and
> > over how the results are displayed via header arguments. There is no
> > such thing in Jupyter notebooks. Controlling the precise appearance of
> > a document produced by Jupyter is much more difficult. Going farther,
> > one can even say that Jupyter notebooks are designed primarily to be
> > read as Jupyter notebooks; exporting to other formats is kind of an
> > afterthought. In contrast, Rmarkdown is designed to produce the final
> > readable result in another format (.html or .pdf typically).
> >
> > Rmarkdown is based on markdown, a human readable markup language,
> > Jupyter notebooks are based on JSON, a data interchange format common
> > on the web. This means that Rmarkdown files can be easily edited using
> > any text editor you like. The same is not true of Jupyter notebooks.
> > While you can of course edit the JSON directly, the format is designed
> > to be written and read by a computer; editing it yourself is not easy.
> >
> > 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.
> >
> > 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.
>
> There are ways to put Shiny apps into Rmarkdown documents; see
> <https://beta.rstudioconnect.com/content/2671/Combining-Shiny-R-Markdown.html>.
>   Other than my two notes above, your comments about Rmarkdown seem
> right on the mark.
>
> Duncan Murdoch
>
> >
> >>
> >>
> >>         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".
> >>
> >> ______________________________________________
> >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >
> > ______________________________________________
> > R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>

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