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

[David Winsemius]

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