[R] Rstudio: is it possible to create a document out of a working script?

[Luca Cerone]

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 <dwinsemius at 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.boh at 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.cerone at 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 at 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 at 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