[R] [Pkg-Collaboratos] BioShapes Almost-Package

[Martin Maechler]

>>>>> 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 using 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 using 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 using 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 using 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 using 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.