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 at 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 at 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]]