[R] Include pre-existing PDF files as vignettes in an R package?

[Michael Hannon]

Exporting to LaTeX is a good idea.  Thanks, guys.


On Mon, Feb 19, 2018 at 4:22 AM, stephen sefick <ssefick at gmail.com> wrote:
> Yes, 'C-c C-e l l' I think, but follow the pop-up, and everything should be
> ok.
>
> On Feb 19, 2018 07:05, "Rainer Krug" <rainer_krug at icloud.com> wrote:
>
>>
>>
>> > On 19 Feb 2018, at 12:25, Duncan Murdoch <murdoch.duncan at gmail.com
>> <mailto:murdoch.duncan at gmail.com>> wrote:
>> >
>> > On 19/02/2018 5:47 AM, Michael Hannon wrote:
>> >> Thanks, Duncan.  The files in question are Emacs Org-mode files, and I
>> >> think these are more or less isomorphic to Rmd files, but I haven't
>> >> used Org-mode in a long time, so I think the mapping (Org-mode ==>
>> >> Rmd) would be painful.
>>
>> That should be easy - you can export org-mode files directly to LaTex. I
>> haven’t used org-mode for some time, but I think it is Ctrl - C - E and
>> than follow the prompts (obviously in emacs).
>>
>> Rainer
>>
>>
>> >
>> > If they aren't LaTeX then they won't be able to masquerade as Sweave
>> files, so things are more complicated.
>> >
>> > I think there are two possibilities.  The better but harder one is to
>> write your own "vignette engine".  Section 1.4.2 of the manual describes
>> the process, and ?tools::vignetteEngine describes what is needed in your
>> engine.
>> >
>> > The other possibility is to manually edit an inst/doc/index.html file to
>> include links to your documents.  They won't be treated as vignettes, but
>> at least users will be able to find them.  The other disadvantage of this
>> approach is that you'll need to edit it for all vignettes, not just the
>> strange ones.
>> >
>> > Duncan Murdoch
>> >
>> >
>> >> -- Mike
>> >> On Mon, Feb 19, 2018 at 1:20 AM, Duncan Murdoch
>> >> <murdoch.duncan at gmail.com <mailto:murdoch.duncan at gmail.com>> wrote:
>> >>> On 18/02/2018 9:06 PM, Michael Hannon wrote:
>> >>>>
>> >>>> Greetings.  The group that I work with has just started using the
>> approach
>> >>>> outlined in Karl Broman's handy primer:
>> >>>>
>> >>>>      http://kbroman.org/pkg_primer/pages/vignettes.html <
>> http://kbroman.org/pkg_primer/pages/vignettes.html>
>> >>>>
>> >>>> to create vignettes for a couple of R packages.
>> >>>>
>> >>>> This works fine as long as we have a current Rmd version of the
>> vignette.
>> >>>> But
>> >>>> we have some old PDF documents that we'd like to include as vignettes
>> as
>> >>>> well.
>> >>>> I'd like to know if there's a way to include such PDF files as
>> vignettes.
>> >>>>
>> >>>> We *do* have the source files for the PDF files in question, but it
>> would
>> >>>> be
>> >>>> tedious to convert those source files to Rmd format.
>> >>>>
>> >>>> My first thought was simply to add the PDF files to the .../vignettes
>> >>>> subdirectory and run the devtools::build_vignettes() function
>> (mentioned
>> >>>> in
>> >>>> the Broman tutorial), but that doesn't work.  I.e., the PDF files
>> don't
>> >>>> appear
>> >>>> in the list of vignettes for the package.
>> >>>>
>> >>>> And after running devtools::build_vignettes I see that there's a lot
>> of
>> >>>> additional stuff in:
>> >>>>
>> >>>>      ...lib/R/site-library/<package_name>/...
>> >>>>
>> >>>> so I don't see any obvious way to "fool" R into using the PDF files
>> that
>> >>>> haven't gone through the whole knitr/rmarkdown process.  (Not to
>> mention
>> >>>> that
>> >>>> such an approach would be fragile at best.)
>> >>>
>> >>>
>> >>> You don't say what format the source is, but if it is LaTeX, you just
>> need
>> >>> to add some comments at the beginning, rename ending in .Rnw, and R
>> will
>> >>> recognize plain LaTeX files as Sweave vignettes.
>> >>>
>> >>> See the Writing R Extensions manual, section 1.4.
>> >>>
>> >>> Duncan Murdoch
>> >>>
>> >>>>
>> >>>> Suggestions welcome.  Thanks.
>> >>>>
>> >>>> -- Mike
>> >>>>
>> >>>> ______________________________________________
>> >>>> R-help at r-project.org <mailto:R-help at r-project.org> mailing list --
>> To UNSUBSCRIBE and more, see
>> >>>> https://stat.ethz.ch/mailman/listinfo/r-help <
>> https://stat.ethz.ch/mailman/listinfo/r-help>
>> >>>> PLEASE do read the posting guide
>> >>>> http://www.R-project.org/posting-guide.html
>> >>>> and provide commented, minimal, self-contained, reproducible code.
>> >>>>
>> >>>
>> >
>> > ______________________________________________
>> > R-help at r-project.org <mailto:R-help at r-project.org> mailing list -- To
>> UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help <
>> https://stat.ethz.ch/mailman/listinfo/r-help>
>> > PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>>
>> --
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
>> Biology, UCT), Dipl. Phys. (Germany)
>>
>> University of Zürich
>>
>> Cell:       +41 (0)78 630 66 57
>> email:      Rainer at krugs.de <mailto:Rainer at krugs.de>
>> Skype:      RMkrug
>>
>> PGP: 0x0F52F982
>>
>>
>>
>>
>>         [[alternative HTML version deleted]]
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/
>> posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.