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

Luca Cerone luca.cerone at gmail.com
Fri Jun 20 11:40:23 CEST 2014

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.

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).


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
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> --
> Bob O'Hara
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Luca Cerone

Tel: +34 692 06 71 28
Skype: luca.cerone

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