publishing knitr or Jupyter docs on web

[Bob Carpenter]

knitr
------------

OK, I didn't realize that when I to this:

> knit("foo.Rmd")

it produces a markdown file and directory of figures:

foo.md
figure/*.png

The figures were only 100K and 40K.

The markdown can be hosted directly on GitHub. Then when
you view the file, GitHub will do the translation from
markdown (.md) to HTML.

See the second example here for a demo:

http://yihui.name/knitr/demo/minimal/

But I don't know how to get the LaTeX to render. If I just
push it and look at in the branch, here's what I get:

https://github.com/stan-dev/example-models/blob/issue-34-case-study-egs/knitr/efron-morris/pool-no-pool.md

No rendering. And it looks like GitHub doesn't want to
render MathJax due to security concerns (don't know what
those are).

Another option is to use pandoc directly to generate HTML.
I'm guessing that's what Rstudio is doing. And Rstudio is
getting the MathJax to work.

I looked up MathJax, and it's primarily client-side. They just
released 2.6 (as in today!):

https://www.mathjax.org/mathjax-v2-6-now-available/

which has server-side support. But unless we run our own servers,
I don't see how that's going to help.


Jupyter
-------

I should probably figure out how to use Jupyter. Could someone else
see what it produces for output? We don't want to host modifiable or
runnable Jupyter docs on mc-stan.org, just HTML (or .md that converts
to HTML) that we can read. Then we want to make the source available.


- Bob

[Jeffrey Arnold]

For the knitr, you'd have to compile to the markdown files to HTML and then host the pages on the gh-pages branch of the repository. Then the mathjax will do the work. If you use rmarkdown it will do most of that for you, and include the figures as Base64 encoded data.

- Bob

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[Bob Carpenter]

Thanks --- I just needed to install pandoc on my
system path and then when I restarted R I could
run

> render("foo.md")

and it produced one of those monster HTML files. Cool.

But it was 850KB, which is a bummer because it was just
150KB or so of pngs pre-conversion. And the math seems to
be being stored as MathJax, not images --- it's nice and crisp,
unlike the images (which are too small coming out of knitr).

- Bob

[Allen B. Riddell]

On 12/30, Jeffrey Arnold wrote:
> For the knitr, you'd have to compile to the markdown files to HTML and then
> host the pages on the gh-pages branch of the repository. Then the mathjax
> will do the work. If you use rmarkdown it will do most of that for you, and
> include the figures as Base64 encoded data.
>

You can setup travis or jenkins to do this (compile + push to the
gh-pages branch) automatically.

[Ben Goodrich]

On Wednesday, December 30, 2015 at 6:21:51 PM UTC-5, Bob Carpenter wrote:

Thanks --- I just needed to install pandoc on my
system path and then when I restarted R I could
run

> render("foo.md")

and it produced one of those monster HTML files.  Cool.

But it was 850KB, which is a bummer because it was just
150KB or so of pngs pre-conversion.  And the math seems to
be being stored as MathJax, not images --- it's nice and crisp,
unlike the images (which are too small coming out of knitr).

Specify

output: 
  html_document: 
    self_contained: no

in the header of the .Rmd file. Possibly also specify fig.path in the setup chunk.

Ben