Re: [O] org-mode vs pandoc export

[Emmanuel Charpentier]

I suppose that you need org-mode to use Babel features (code and/or
code execution results intermixed with your paper's text).

I have had trouble with .dot exporting using the builtin .dot exporter,
but can't, for the life of me, remembering if my troubles were cross-
reference or citations-related (an academic paper usually needs
both...). I noted that the references done via John Kitchin's excellent
org-ref didn't export to .dot.

As far as I can tell, ox-pandoc does its own numbering (generating an
intermediate temporary file that I never managed to catch) and does not
use  pandoc-crossref.

ISTR that a "clever" use of org-ref allows to number equations... in
LaTeX output. I also STR that it doesn't work in .docx output. John
Kitchin (the org-ref author) thinks that the key is to generate a
correct \LaTeX file and to export that to .docx via pandoc.

At this point, writing a \LaTeX file with pandoc export in mind is
probably your best bet. There exist (limited) alternatives to the 
Babel features of org-mode:
 - knitr (supports R and Python code in "session"mode, i. e. continuity
between code chunks),
 - SageTeX (post-processing in a single Sagemath run ; can include code
for a variety of math software, including R),
 - Pythontex (postprocessor, supports Python, Sage, Octave and a couple
other, but not R ; a clever use of knitr and Pythontex is possible).

Possible alternative: Markdown + Codebraid (supports a hanful of
langiages, including R and (development branch) Sage). This should
accept pandoc-crossref numbering. But it's Markdown, with limited
formatting abilities...

So, we have an array of partial solutions, none universal. Pick your
poison...

Out of curiosity: in which domain still exist journal publishers not
accepting \LaTeX ? I suspect medicine...

HTH,

--
Emmanuel Charpentier