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 <dwinsem...@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....@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. > > David Winsemius > Alameda, CA, USA > -- 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.