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

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).

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

--
Bob O'Hara

Biodiversity and Climate Research Centre
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Germany

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--
Luca Cerone

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Skype: luca.cerone