>>>>> Jeff Newmiller >>>>> on Sun, 03 Sep 2023 19:47:32 -0700 writes:
> Leonard... the reason roxygen exists is to allow markup in > source files to be used to automatically generate the > numerous files required by standard R packages as > documented in Writing R Extensions. If your goal is to > not use source files this way then the solution is to not > use roxygen at all. Just create those files yourself by > directly editing them from scratch. Yes. Many experienced R programmers do not use Roxygen (or use it only rarely; e.g., together with ESS (Emacs Speaks Statistics) to make the initial creation or sometime a thorough updating the help pages man/*.Rd more convenient). There are different tastes and different work flows for different people. Martin > On September 3, 2023 7:06:09 PM PDT, Leonard Mada via > R-help <r-help@r-project.org> wrote: >> Thank you Bert. >> >> >> Clarification: >> >> Indeed, I am using an add-on package: it is customary for >> that package - that is what I have seen - to have the >> entire documentation included as comments in the R src >> files. (But maybe I am wrong.) >> >> >> I will try to find some time over the next few days to >> explore in more detail the R documentation. Although, I >> do not know how this will interact with the add-on >> package. >> >> >> Sincerely, >> >> >> Leonard >> >> >> On 9/4/2023 4:58 AM, Bert Gunter wrote: >>> 1. R-package-devel is where queries about package >>> protocols should go. >>> >>> 2. But... "Is there a succinct, but sufficiently >>> informative description of documentation tools?" >>> "Writing R Extensions" (shipped with R) is *the* >>> reference for R documentation. Whether it's sufficiently >>> "succinct" for you, I cannot say. >>> >>> "I find that including the documentation in the source >>> files is very distracting." ?? R documentation (.Rd) >>> files are separate from source (.R) files. Inline >>> documentation in source files is an "add-on" capability >>> provided by optional packages if one prefers to do >>> this. Such packages parse the source files to extract >>> the documentation into the .Rd files/ So not sure what >>> you mean here. Apologies if I have misunderstood. >>> >>> " I would prefer to have only basic comments in the >>> source files and an expanded documentation in a separate >>> location." If I understand you correctly, this is >>> exactly what the R package process specifies. Again, see >>> the "Writing R Extensions" manual for details. >>> >>> Also, if you wish to have your package on CRAN, it >>> requires that the package documents all functions in the >>> package as specified by the "Writing ..." manual. >>> >>> Again, further questions and elaboration should go to >>> the R-package-devel list, although I think the manual is >>> really the authoritative resource to follow. >>> >>> Cheers, Bert >>> >>> >>> >>> On Sun, Sep 3, 2023 at 5:06 PM Leonard Mada via R-help >>> <r-help@r-project.org> wrote: >>> >>> Dear R-List Members, >>> >>> I am looking for collaborators to further develop the >>> BioShapes almost-package. I added a brief description >>> below. >>> >>> A.) BioShapes (Almost-) Package >>> >>> The aim of the BioShapes quasi-package is to facilitate >>> the generation of graphical objects resembling >>> biological and chemical entities, enabling the >>> construction of diagrams based on these objects. It >>> currently includes functions to generate diagrams >>> depicting viral particles, liposomes, double helix / DNA >>> strands, various cell types (like neurons, brush-border >>> cells and duct cells), Ig-domains, as well as more basic >>> shapes. >>> >>> It should offer researchers in the field of biological >>> and chemical sciences a tool to easily generate diagrams >>> depicting the studied biological processes. >>> >>> The package lacks a proper documentation and is not yet >>> released on CRAN. However, it is available on GitHub: >>> https://github.com/discoleo/BioShapes >>> >>> Although there are 27 unique cloners on GitHub, I am >>> still looking for contributors and collaborators. I >>> would appreciate any collaborations to develop it >>> further. I can be contacted both by email and on GitHub. >>> >>> >>> B.) Documentation Tools >>> >>> Is there a succinct, but sufficiently informative >>> description of documentation tools? I find that >>> including the documentation in the source files is very >>> distracting. I would prefer to have only basic comments >>> in the source files and an expanded documentation in a >>> separate location. >>> >>> This question may be more appropriate for the >>> R-package-devel list. I can move the 2nd question to >>> that list. >>> >>> ### >>> >>> As the biological sciences are very vast, I would be >>> very happy for collaborators on the development of this >>> package. Examples with existing shapes are available in >>> (but are unfortunately not documented): >>> >>> Man/examples/Examples.Man.R R/Examples.R >>> R/Examples.Cells.R tests/experimental/* >>> >>> >>> Many thanks, >>> >>> Leonard >>> >>> ______________________________________________ >>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and >>> more, see https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide >>> http://www.R-project.org/posting-guide.html >>> <http://www.R-project.org/posting-guide.html> and >>> provide commented, minimal, self-contained, reproducible >>> code. >>> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and >> more, see 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. > -- > Sent from my phone. Please excuse my brevity. > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and > more, see 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 -- To UNSUBSCRIBE and more, see 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.