On Thu, Oct 7, 2010 at 5:12 PM, Erik Iverson wrote: > > Dan Davison wrote: > >> Erik Iverson writes: >> >> Rainer M Krug wrote: >>> >>>> Hi >>>> >>>> I am about to write an R package, and as I am an org-mode and >>>> org-babel user, I would (obviously) like to use org-mode for that. >>>> >>>> Is there a recommended way of writing an R package in org-babel, or >>>> do I have effectively wrap the R code for the documentation >>>> etc. into source blocks in babel? >>>> >>> That's what I do. I've looked into converting an org-file to >>> Roxygen or Rd markup, but never got very far. My idea at the time >>> was to do something like: >>> >>> * function1 >>> ** Help >>> *** Title >>> this is function 1 title >>> *** Description >>> function1 does this... >>> *** Usage >>> function1(arg1, arg2, ...) >>> *** Arguments >>> arg1: the first argument >>> *** Examples >>> function1(arg1 = x, arg2 = y) >>> **Definition >>> begin_src R :tangle R/package.R >>> function1 <- function(arg1, arg2) { >>> >>> } >>> >>> I like the idea of a kind of template, which takes the function name as a parameter and expands it to the above described structure, but also including one section for tests. That would definitely be a starting point from which one could look into the "problem" of the .Rd files. As I am not an emacs / elisp expert, how could that be done (the template)? > >>> Any suggestions how to best proceed? >>>> >>>> Dream: I would like to have one org file which contains everything >>>> (documentation, code, other relevant files) and if I export or >>>> tangle the file, I have the package ready. >>>> >>> Well, that functionality is essentially present with code blocks >>> and tangling, except the documentation part. >>> >> Exactly - and that is the part I would like to have. > >> Hi Erik, >> >> Would you mind expanding on that -- what are we missing for the >> documentation part? >> >> > Dan, by "except for the documentation part", I meant generating > .Rd files (the LaTeX-like syntax) automatically from some org-syntax > that does *not* depend on code blocks. I.e., it would be cool to > specify syntax like I have above for documentation. Using org-mode > headlines for each section like Description, Usage, Arguments, etc. > > Just like exporting to LaTeX generates sections, some process would > use these headlines to generate the .Rd sections. > > That way, you don't have to use the .Rd syntax yourself. No big deal, > just a convenience feature. I don't know how you'd specify to org-mode > that a particular subtree was to generate .Rd syntax, and I don't know > if it would be on export or tangling. > > An alternative is simply just to use code blocks of type Rd within > org-mode and then tangle to .Rd files. That's what I currently do. > > Hope that explains it, > Erik > > > Dan >> > -- NEW GERMAN FAX NUMBER!!! Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax: +27 - (0)86 516 2782 Fax: +49 - (0)321 2125 2244 email: Rainer@krugs.de Skype: RMkrug Google: R.M.Krug@gmail.com