[R] RMarkdown vignettes v. Jupyter notebooks?

Ista Zahn |@t@z@hn @end|ng |rom gm@||@com
Thu Oct 11 16:11:44 CEST 2018 

On Thu, Oct 11, 2018 at 10:03 AM Jeff Newmiller
<jdnewmil using dcn.davis.ca.us> wrote:
>
> Ista, you do not seem to be aware of the
> .nb.html format, which is way easier to share with a non-uswr than an ipynb file yet allows the same in-progress kinds of results to be shared and the source can be extracted easily using a web browser (no server needed).

Yes, I am aware that notebooks can be exported / converted to other
formats, including .html and .pdf. My point is about emphasis:
Rmarkdown gives you header arguments and other tools that allow you a
great deal of control over how the final .html or .pdf file looks. The
system seems designed to produce .html or .pdf as the final output
format. Jupyter notebooks on the other hand seem primarily designed to
be viewed as Jupyter notebooks: they don't give you a log of tools for
controlling how the converted / exported notebook appears. That's not
so say there is not conversion / export possible of course...

--Ista

>
> There is some controversy about this whole notebook approach [1] but I think deciding whether it is right for your purposes is highly subjective.
>
> FWIW It took me years to figure out how to even open a Jupyter notebook, so the idea that they should be the gold standard for sharing results seems absurd to me.
>
> [1] https://yihui.name/en/2018/09/notebook-war/
>
> On October 11, 2018 5:53:29 AM PDT, Ista Zahn <istazahn using gmail.com> wrote:
> >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.
> >> >
> >>
> >
> >______________________________________________
> >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.
>
> --
> Sent from my phone. Please excuse my brevity.

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