[Rd] Concordances in R Markdown

[Duncan Murdoch]

Two quick updates:

I will (probably) merge the Markdown support code into the patchDVI 
package (currently in the RmdConcord branch), instead of creating a new 
package.  So install instructions should be:

    devtools::install_github("dmurdoch/backports")
    devtools::install_github("dmurdoch/knitr")
    devtools::install_github("dmurdoch/patchDVI using RmdConcord")

I need to finish some integration with patchDVI and finalize my decision 
before merging that code into the main branch of patchDVI, but it's 
basically working now.

Secondly, with John Nash's help, I've identified some important 
limitations of the current Pandoc support.  Most importantly, Markdown 
citations (e.g. [@doe99]) are not handled.  Apparently this extension is 
being worked on, but there's no predicted completion date.  All the 
limitations that I know about are now documented in the patchDVI vignette.

Duncan Murdoch

On 26/11/2022 8:54 a.m., Duncan Murdoch wrote:
> I submitted some code to support concordances to R-devel, and wrote this
> blog article about it:
> 
>     https://blog.r-project.org/2022/10/20/concordances/index.html
> 
> (Concordances are links from a source file to pre-processed output from
> Sweave or knitr.)
> 
> In the article I said "as far as I know, Pandoc doesn’t support any way
> to relate input lines to output lines", and asked to be corrected if
> that was wrong.  I was corrected!  Heather Turner pointed me in the
> direction of this:
> 
>    https://github.com/jgm/pandoc/issues/4565#issuecomment-749294039
> 
> She also worked out the initial details of how to make use of it.
> Thanks Heather!
> 
> I have now put together a package called RmdConcord (see
> https://github.com/dmurdoch/RmdConcord) which exports R Markdown drivers
> that incorporate concordances.  This means that previewers like TeXworks
> that support Synctex will now synchronize the output with the true
> input, which makes editing a lot easier.  If you have complaints from
> HTML Tidy about your vignettes, they should also refer to the original
> source now.
> 
> The package requires changes to the knitr package to support
> concordances in R Markdown documents, and to the backports package to
> support the R-devel concordance additions in earlier versions of R.
> I've submitted pull requests to both packages to include these changes,
> but in the meantime, you will need to install my devel versions of them:
> 
>     devtools::install_github("dmurdoch/backports")
>     devtools::install_github("dmurdoch/knitr")
>     devtools::install_github("dmurdoch/RmdConcord")
> 
> If anyone is interested in testing this, I'd appreciate bug reports and
> suggestions.
> 
> Duncan Murdoch