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

[Leonard Mada]

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
>
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