Re: [O] How to write medical journal articles with org-mode

[Erik Hetzner]

At Mon, 20 Jan 2014 14:04:24 -0500,
regcl wrote:
> 
> Erik Hetzner <address@hidden> writes:
> 
> > At Mon, 20 Jan 2014 02:54:08 -0500,
> > regcl wrote:
> >> 
> >> 3) How do I get references into MS word?
> >> 
> > Hi George,
> >
> > For question 3, you might have a look at pandoc
> > (http://johnmacfarlane.net/pandoc/), which can convert from markdown
> > to docx (MS Word) with citation support. You might find it simpler to
> > export from org-mode to markdown and use pandoc to produce your docx
> > files, thus saving some steps above.
> >
> > best, Erik
> 
> Hi Erik, Thank you for the suggestion.  
> 
> WRT this approach, I see that Rick Frankel has said ...
> 
> > From:        Rick Frankel
> > Subject:     Re: [O] Org Table Export to Markdown Table Question
> > Date:        Thu, 09 Jan 2014 11:58:37 -0500
> >
> > > On 2014-01-08 15:41, Aric wrote:
> > > I am trying to use org-mode now with R code in it to write
> > > manuscripts. That does unfortunately mean that it must be eventually
> > > exported to some doc format. I have been able to export to markdown and
> > > everything looks good in markdown (even previewed on github) with the
> > > exception of latex code which is not converted. However, using pandoc to
> > > convert the markdown to docx, the tables are not converted properly (all
> > > a single column).
> > 
> > I'm not sure why you are using markdown as an intermediate file
> > format. Org will export to latex, pdf (via latex) and openoffice odt
> > (which can be exported from open/libre office to doc/docx.).
> > 
> > Both the above exporters are much more mature that the markdown
> > exporter.
> > 
> > rick
> > 
> 
> ... which makes me wonder... Has anyone out there tried this for a
> journal manuscript with figures, tables, and citations?
> 
> If I want go with pandoc, would I be ahead to do ...
> 
> org > latex > pandoc > docx ?
> 
> Thanks, George

Hi George,

pandoc has very rich citation citation support, much better than
org-mode as far as I know. If you are exporting to LaTeX you can use
BibTeX or BibLaTeX which of course work well, but pandoc can handle
citation export to docx, odt, etc. using any citation style supported
by citeproc.

The problem is that org-mode exports tables in markdown as HTML
tables, not pandoc tables. It should be possible to modify the ox-md
exporter to support pandoc tables, but it looks a little tricky.

pandoc’s standard input is markdown, so you’re probably best sticking
with that, but you might be able to get org -> latex -> pandoc -> docx
to work.

best, Erik

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