Hi Jeff,
so far I have used the knitr purl() function, which extracts all the
code chunks in a single R script.
To achieve exactly what I need, the documentation at rmarkdown.rstudio.com seems
to imply that playing with formats would allow me to get the report
out of an existing
script, but I still haven't tested that.
Hope this helps,
Cheers,
Luca
2014-06-21 15:47 GMT+02:00 Jeff Newmiller <jdnew...@dcn.davis.ca.us>:
> As much as I admire RStudio for making these documentation formats easy to
> use, they did not invent any of them. The closest they came to that was
> hiring Yihui.
>
> Having occupied our time with your questions, it would be polite if you
> closed the topic by explaining which approach you settled on and why.
> ---------------------------------------------------------------------------
> Jeff Newmiller The ..... ..... Go Live...
> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go...
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> ---------------------------------------------------------------------------
> Sent from my phone. Please excuse my brevity.
>
> On June 21, 2014 2:05:08 AM PDT, Luca Cerone <luca.cer...@gmail.com> wrote:
>>Dear all thank you very much for all the advices and help :)
>>I think that Rstudio formats do what I need!
>>
>>
>>
>>2014-06-21 3:31 GMT+02:00 David Winsemius <dwinsem...@comcast.net>:
>>>
>>> On Jun 20, 2014, at 2:40 AM, Luca Cerone wrote:
>>>
>>>> Hi Berend, sorry if it OT (though I think that the process is pretty
>>>> much Rstudio independent, since what Rstudio does is wrap up knitr
>>and
>>>> their package Rmarkdown,
>>>> but all the process can be run from the shell).
>>>>
>>>> Bob, so far this is what I do, but it is not ideal for two reasons:
>>>> 1. I would like my report to be a step by step guide of what the
>>>> script does. Wrapping the scripts in small functions, subscripts
>>>> doesn´t help,
>>>> because in the report what you would see is "source("subscript.r"),
>>>> not the content of the subscript.
>>>
>>> Have you looked at ?source and considered changing the associated
>>option?
>>>
>>>> getOption("verbose")
>>> [1] FALSE
>>>
>>>>
>>>> 2. in a way I would need the exact opposite of what knitr and
>>>> Rmarkdown do (at least by default). I would like to document my
>>script
>>>> in a way that can be run independently of the report and that, when
>>>> neede, could use the comments to generate the report, similarly to
>>how
>>>> roxygen2 works when writing the documentation.
>>>>
>>>> Thanks a lot for the help,
>>>> apologies again if this is OT (if so please remove the thread and I
>>>> will ask in the the Rstudio support).
>>>>
>>>> Cheers,
>>>> Luca
>>>>
>>>> 2014-06-20 11:28 GMT+02:00 Bob O'Hara <rni....@gmail.com>:
>>>>> How about simply using source() to call the script? If necessary,
>>wrap bits
>>>>> of the script in functions, so you source a file with lots of
>>functions, and
>>>>> then call the ones you need, as you need them.
>>>>>
>>>>> Bob
>>>>>
>>>>> On 20 June 2014 11:20, Luca Cerone <luca.cer...@gmail.com> wrote:
>>>>>>
>>>>>> Dear all,
>>>>>> I am very happy with the new features introduced by Rstudio about
>>how
>>>>>> to create documents embedding R code.
>>>>>>
>>>>>> I would like to know though if there is some way to embed code
>>from a
>>>>>> working script into an Rmd document.
>>>>>> I have several working scripts for which I would like to report
>>the
>>>>>> results, but I would like to avoid
>>>>>> copy and paste the code in the Rmd document: the pipeline is still
>>a
>>>>>> work in progress,
>>>>>> and it is likely that I will end up changing the code and
>>parameters
>>>>>> in the script.
>>>>>>
>>>>>> As you can imagine, having to copy and paste my code is prone
>>error,
>>>>>> and leads to a lot of code replication.
>>>>>> I would like to avoid this, but couldn´t find a straightforward
>>way so
>>>>>> far.
>>>>>>
>>>>>>
>>>>>> Thanks a lot in advance,
>>>>>> of course if you have other advices, or comments on best practices
>>for
>>>>>> this sort of thing,
>>>>>> I would like to hear them from you.
>>>>>>
>>>>>> Cheers,
>>>>>> Luca
>>>>>>
>>>>>> ______________________________________________
>>>>>> R-help@r-project.org mailing list
>>>>>> 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.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Bob O'Hara
>>>>>
>>>>> Biodiversity and Climate Research Centre
>>>>> Senckenberganlage 25
>>>>> D-60325 Frankfurt am Main,
>>>>> Germany
>>>>>
>>>>> Tel: +49 69 798 40226
>>>>> Mobile: +49 1515 888 5440
>>>>> WWW: http://www.bik-f.de/root/index.php?page_id=219
>>>>> Blog: http://occamstypewriter.org/boboh/
>>>>> Journal of Negative Results - EEB: www.jnr-eeb.org
>>>>
>>>>
>>>>
>>>> --
>>>> Luca Cerone
>>>>
>>>> Tel: +34 692 06 71 28
>>>> Skype: luca.cerone
>>>>
>>>> ______________________________________________
>>>> R-help@r-project.org mailing list
>>>> 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.
>>>
>>> David Winsemius
>>> Alameda, CA, USA
>>>
>>
>>
>>
>>--
>>Luca Cerone
>>
>>Tel: +34 692 06 71 28
>>Skype: luca.cerone
>>
>>______________________________________________
>>R-help@r-project.org mailing list
>>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.
>
--
Luca Cerone
Tel: +34 692 06 71 28
Skype: luca.cerone
______________________________________________
R-help@r-project.org mailing list
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.
