On Thu, Oct 11, 2018 at 10:23 AM Yihui Xie <x...@yihui.name> wrote: > > In case Jeff's point was not clear enough: the *.nb.html file is very > similar to *.ipynb and it is very different with other output formats > that R Markdown generates. A .nb.html file is generated alongside .Rmd > when you preview an R Markdown notebook, and it contains both the R > Markdown source document and its output (in a single file). See > Section 3.2.2 of the R Markdown book for more info: > https://bookdown.org/yihui/rmarkdown/notebook.html
Thank you Yihui, you have once again rescued me from a state of ignorance. Much appreciated. --Ista > > But I think you are correct that R Markdown and Jupyter have different > emphasis. > > Regards, > Yihui > -- > https://yihui.name > > On Thu, Oct 11, 2018 at 9:14 AM Ista Zahn <istaz...@gmail.com> wrote: > > > > On Thu, Oct 11, 2018 at 10:03 AM Jeff Newmiller > > <jdnew...@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 <istaz...@gmail.com> wrote: > > > >On Thu, Oct 11, 2018 at 8:36 AM Duncan Murdoch > > > ><murdoch.dun...@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.gra...@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-l...@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@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@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@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. > > > > ______________________________________________ > > R-help@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@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.
