On Fri, Jun 20, 2014 at 2:40 AM, Luca Cerone <luca.cer...@gmail.com> 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.
>
> 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.http://rmarkdown.rstudio.com/r_notebook_format.html /Henrik > > 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. ______________________________________________ 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.
