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

[Jeff Newmiller]

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.

On September 3, 2023 7:06:09 PM PDT, Leonard Mada via R-help 
 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 
>>  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
>> 
>> and provide commen

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

[Leonard Mada via R-help]

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 
>  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
> 
> 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.

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

[Bert Gunter]

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 
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
> 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.

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

[Leonard Mada via R-help]

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
and provide commented, minimal, self-contained, reproducible code.