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Re: [O] Babel R source blocks problem

From: Thomas S. Dye
Subject: Re: [O] Babel R source blocks problem
Date: Mon, 13 Mar 2017 12:37:29 -1000
User-agent: mu4e 0.9.17; emacs 25.1.1

Aloha Chuck,

Charles C. Berry writes:

> On Fri, 10 Feb 2017, Thomas S. Dye wrote:
>> Aloha Chuck,
>> Charles C. Berry writes:
>>> A look at the `slidify-example.org' file in the `org-9-plus' branch of my
>>> (chasberry) `orgmode-accessories' github repo might be a good start with
>>> .Rmd exports even if you do not want to use `slidify'.
>> Your ox-ravel exporter is a pleasure to use.  I'm farther along than I
>> thought I'd be at this point.
> Thanks. I am glad to hear this.
>> I'm new to much of the R ecosystem, including slidify, so forgive some
>> noob ignorance in the following three questions:
>> 1) I've specified the properties EXPORT_TITLE and EXPORT_AUTHOR, but
>> they don't show up in the .Rmd file.  Is this a limitation of ox-ravel,
>> or do I need to learn how to insert them in the Org mode source?
> Both, I guess.
> Arguably, it is a limitation in the markdown backends available that
> there isn't one that will create the yaml header from the export
> options in the org buffer.  I think the long term fix is to create a
> backend derived from 'md, but this is far down my todo list.  For now,
> either hand tool a yaml header like that in
> : slidify-example.org::#tds-headline
> (If you are viewing that on my github repo, be sure to click 'raw' or the
> yaml header will not be visible!)
> or create a src block that will pull the title, author, et cetera and wrap
> them as a yaml header in an md export block and put it at the top of the
> output. If you want to do the src block, I can provide a skeleton version.
>> 2) How do I instruct ox-ravel to include the graphics output of a source
>> code block?  I tried :ravel fig=TRUE as a header to the source code
>> block, but no dice.  Most of my experience is with ox-latex, so that
>> colors my expectations here; i.e. I'm expecting a [[file:myfile.pdf]]
>> link to produce a graphic in the output.
> Often it `just works', but it depends on the vignette engine. `fig=TRUE'
> is correct for Sweave. See
> : demos.org::#36234656-157D-4F1D-B441-E727DFCC0251
> for an example of that. For knitr, you usually do not need to include
> anything if there is just one plot produced, but there are loads of
> options. See
>       https://yihui.name/knitr/options/#plots
> I find myself using ~:ravel fig.cap=my_caption~ (where `my_caption' is
> an R string from an earlier src block) a lot. See
> : demos.org::#C341969B-90F3-4C27-AA7F-5352A9669506
> for an example of a lengthy caption done in latex.
> There is a src block that produces a plot in the slidify-example.org file.
> No special header was needed for ~slidify()~ to render it.  But I cannot
> be sure whether the yaml block does something special for the graphics.
>> 3) I've been knitting the .Rmd output using RStudio, which is also new
>> to me.  I don't mind doing this (it is what the session organizer is
>> going to do with the .Rmd file I send next week), but I'm wondering
>> if you have an emacs-only solution?
> I don't know RStudio, but here is a start:
> #+BEGIN_SRC R :exports none :results silent
> require(rmarkdown)
> render("my-file.Rmd")
> If you look at the =demos.org= file, you will see examples and the src
> blocks used to run ~knitr::knit2pdf()~.  If you export some of the
> examples to *.Rmd files and run the equivalent ~render(...)~ on the .Rmd
> files, you will get html by default.
> ---
> Let me know how it works out!

Just a short note to let you know that ox-ravel was a terrific tool for
my project of producing a workable R Markdown file for an upcoming
conference.  I was dreading the requirement to provide .Rmd source for a
handout, but ox-ravel made it one of the easiest steps.

Thanks for your contribution to Org mode and your support when I was
flailing around last month.

All the best,

Thomas S. Dye

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