R help - Feb 2018 - Include pre-existing PDF files as vignettes in an R package?

> 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 Z?rich

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]]

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 Z?rich
>
> 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]]

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 Z?rich
>>
>> 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.