Rpolyhedra

[kenarab]

Submitting Author: Alejandro Baranek" (@kenarab)
Repository: https://github.com/qbotics/Rpolyhedra
Version submitted: 0.1.0
Editor: @noamross
Reviewer 1: @yulijia
Reviewer 2: @schloerke
Archive: N/A
Version accepted: 0.4.1

Summary

• What does this package do? (explain in 50 words or less):

A 142 polyhedra Database scraped from PHD as R6 objects and RGL visualizing capabilities. The PHD format was created to describe the geometric polyhedron definitions derived mathematically by Andrew Hume and by the Kaleido program of Zvi Har'El.

• Paste the full DESCRIPTION file inside a code block below:

Package: Rpolyhedra
Type: Package
Title: Polyhedra Database
Version: 0.1.0
Authors@R: c(
    person("Alejandro", "Baranek",,"abaranek@dc.uba.ar", c("aut","com","cre", "cph")),
    person("Leonardo","Belen",,"leobelen@gmail.com", c("aut","com","cph"))
    )
Maintainer: Alejandro Baranek <abaranek@dc.uba.ar>
Description: A 142 polyhedra database scraped from PHD files <http://paulbourke.net/dataformats/phd/> as R6 objects and 'rgl' visualizing capabilities. The PHD format was created to describe the geometric polyhedra definitions derived mathematically <http://www.netlib.org/polyhedra/> by Andrew Hume and by the Kaleido program of Zvi Har'El.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown,
    covr
VignetteBuilder: knitr
Depends: R (>= 3.0.0)
Imports: futile.logger,
         rgl,
         stringr,
         R6,
         testthat
Collate:
  'polyhedra-lib.R'
  'zzz.R'
BugReports: https://github.com/qbotics/Rpolyhedra/issues

• URL for the package (the development repository, not a stylized html page):
  https://github.com/qbotics/Rpolyhedra

• Please indicate which category or categories from our package fit policies this package falls under *and why(? (e.g., data retrieval, reproducibility. If you are unsure, we suggest you make a pre-submission inquiry.):

[e.g., "data extraction, because the package parses a scientific data file format"]

data retrieval, because includes the code for downloading the phd files
data extraction, because the package parses a scientific data file format
database access, because it gives access to PHD polyhedra database

Other categories:
legacy sourcecode: as poly is an opensource inciative (from '80s) than no longer compiles, the project gives access to original poly outputs.

• Who is the target audience?

  • Scientists and general public who wants to explore polyhedra through RGL.
  • Scientists and general public who wants to study polyhedra's properties and make taxonomies
  • Scientists and general public who wants to make models over polyhedra definitions

• Are there other R packages that accomplish the same thing? If so, how does
  yours differ or meet our criteria for best-in-category?

RGL includes 5 regular solids. Rpolyhedra provides version of the 5 regular solids and 137 more polyhedra.

Requirements

Confirm each of the following by checking the box. This package:

• does not violate the Terms of Service of any service it interacts with.
• has a CRAN and OSI accepted license.
• contains a README with instructions for installing the development version.
• includes documentation with examples for all functions.
• contains a vignette with examples of its essential functions and uses.
• has a test suite.
• has continuous integration, including reporting of test coverage, using services such as Travis CI, Coeveralls and/or CodeCov.
• I agree to abide by ROpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

Publication options

• Do you intend for this package to go on CRAN?
• Do you wish to automatically submit to the Journal of Open Source Software? If so:
  • The package has an obvious research application according to JOSS's definition.
  • The package contains a paper.md matching JOSS's requirements with a high-level description in the package root or in inst/.
  • The package is deposited in a long-term repository with the DOI:
  • (Do not submit your package separately to JOSS)

Detail

• Does R CMD check (or devtools::check()) succeed? Paste and describe any errors or warnings:

• Does the package conform to rOpenSci packaging guidelines? Please describe any exceptions:

• If this is a resubmission following rejection, please explain the change in circumstances:

• If possible, please provide recommendations of reviewers - those with experience with similar packages and/or likely users of your package - and their GitHub user names:

• Delete the file inst/extdata/polyhedra.RDS for scraping and regenerating it.
• Compile the package with a small number of polyhedra first:

.polyhedra <- scrapePolyhedra(max.quant = 5, test = FALSE)

• We have to find a way for accelerate the scraping of the whole database. Maybe a reviewer know a tweak.

[sckott]

thanks for your submission @kenarab

Please change the URL to https://github.com/qbotics/Rpolyhedra/ instead of https://github.com/cran/Rpolyhedra/

We need some clarification to assess fit

• What are the scientific uses of these data? You say scientists are a target audience, but what kind? What would they do with these data?
• I know little about this area. Are there alternative ways to specify polyhedra? If so, what is most widely used?

[kenarab]

Thank you @sckott.

I corrected the URL, and extended the users with this paragraph:

• Scientists and general public who wants to explore polyhedra through RGL.
• Scientists and general public who wants to study polyhedra's properties and make taxonomies
• Scientists and general public who wants to make models over polyhedra definitions

About

• I know little about this area. Are there alternative ways to specify polyhedra? If so, what is most widely used?

PHD is a legacy open source specification for polyhedra. As we found online that database with solid definition we chose to use it for further research over polyhedra.
For specifying polyhedra solids there is only needed to describe vertex and edges (and the definition is not exclusive). But there are different properties the specialists uses: Schaffi symbols, symmetry/rotation groups, etc.

For example, in Wikipedia there are a lot of information. https://en.wikipedia.org/wiki/Icosahedron
The visualizations of wikipedia are generally made in POV-ray.
There is currently no way for accessing a large database of solid (and net) models of polyhedra in R. That's the target of Rpolyhedra.

Rpolyhedra includes algorithms for triangulating polygon faces for producing RGL Models based only in trangles (tmesh).

We didn't work yetwith polyhedra formulation and generation in Rpolyhedra (Is not really our objective). We only give access to other people work, It's a compilation work.
There are private projects with polyhedra databases but RGL includes only models for 5 regular solids as RGL models. That's why we think Rpolyhedra could be useful for R community.

[sckott]

Thank you @kenarab

[sckott]

hi @kenarab thx for your submission - @noamross will be handling editor

[noamross]

Editor checks:

• Fit: The package meets criteria for fit and overlap
• Automated tests: Package has a testing suite and is tested via Travis-CI or another CI service.
• License: The package has a CRAN or OSI accepted license
• Repository: The repository link resolves correctly
• Archive (JOSS only, may be post-review): The repository DOI resolves correctly
• Version (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)?

---

Editor comments

Hi @kenarab, thanks for your submission, I think this is a really neat package. I can think of a few people who would be interested already who I might ask to review. A few things before we can assign reviewers, though:

• We require that packages have continuous integration (typically Travis-CI), and code coverage reporting (typically codecov or coveralls). Looking at your package tests, I see you are testing the scraping functions but not necessarily what goes on in the R6. We don't require 100% code coverage, but we'd like coverage of the major functionality. As far as I can tell there are three major functionalities: scraping the data from netlib, parsing the PHD format, and providing R6 objects with polyhedral data. All three should have associated tests. You can use skip_on_cran() or skip_on_travis() if long-running scraping calls or RGL calls will break that. Let us know if you'd like some pointers to setting this infrastructure set up.
• It looks like you have some debugging infrastructure hard-coded into the package right now via the futile.logger calls. This breaks other testing tools and also results in unneeded/confusing messages bring printed out to the user. This should be removed. You might keep it on a development branch.
• I note that the code doesn't run in your vignette because there isn't a library(rgl) call. You also should consider using the WebGL capability in the rgl package so that you can make a vignette that compiles and shows.
• Documentation is very sparse - most functions have a single sentence. We try to aim documentation to be sufficient for familiars unfamiliar with the original data source. R6 classes can be a bit difficult to document, but docs should detail the arguments and formats of the member functions. We want documentation to be as complete as possible at submission so reviewers can give feedback on it.

[kenarab]

Thank you Noam. Thank you very much for your sharp observations. We are already working on the recommendations and next week will push a new release including the proper changes. Best regards, Alejandro. 2017-11-16 18:18 GMT-03:00 Noam Ross <notifications@github.com>:

…

Editor checks: - *Fit*: The package meets criteria for fit <http://policies.md#fit> and overlap <http://policies.md#fit> - *Automated tests:* Package has a testing suite and is tested via Travis-CI or another CI service. - *License:* The package has a CRAN or OSI accepted license - *Repository:* The repository link resolves correctly - *Archive* (JOSS only, may be post-review): The repository DOI resolves correctly - *Version* (JOSS only, may be post-review): Does the release version given match the GitHub release (v1.0.0)? ------------------------------ Editor comments Hi @kenarab <https://github.com/kenarab>, thanks for your submission, I think this is a really neat package. I can think of a few people who would be interested already who I might ask to review. A few things before we can assign reviewers, though: - We require that packages have continuous integration (typically Travis-CI), and code coverage reporting (typically codecov or coveralls). Looking at your package tests, I see you are testing the scraping functions but not necessarily what goes on in the R6. We don't require 100% code coverage, but we'd like coverage of the major functionality. As far as I can tell there are three major functionalities: scraping the data from netlib, parsing the PHD format, and providing R6 objects with polyhedral data. All three should have associated tests. You can use skip_on_cran() or skip_on_travis() if long-running scraping calls or RGL calls will break that. Let us know if you'd like some pointers to setting this infrastructure set up. - It looks like you have some debugging infrastructure hard-coded into the package right now via the futile.logger calls in you .onLoad(). This breaks other testing tools and also results in unneeded/confusing messages bring printed out to the user. This should be removed. You might keep it on a development branch. - I note that the code doesn't run in your vignette because there isn't a library(rgl) call. You also should consider using the WebGL capability <https://cran.r-project.org/web/packages/rgl/vignettes/WebGL.html> in the *rgl* package so that you can make a vignette that compiles and shows. - Documentation is very sparse - most functions have a single sentence. We try to aim documentation to be sufficient for familiars unfamiliar with the original data source. R6 classes can be a bit difficult to document, but docs should detail the arguments and formats of the member functions. We want documentation to be as complete as possible at submission so reviewers can give feedback on it. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#157 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACzA1qJXuxcKBb4hqWp0yLkuRol1w9XNks5s3Ka4gaJpZM4QYpu6> .

-- alejandro baranek @ken4rab <https://twitter.com/ken4rab> qbotics <http://qbotics.tumblr.com/> | surferinvaders <http://surferinvaders.tumblr.com> | algebraic-soundscapes <http://imaginary.org/content/algebraic-soundscapes> | surfer-shuffle <http://imaginary.org/program/surfer-shuffle>

[noamross]

Any update on this, @kenarab?

[kenarab]

Hello Noam: I'm sorry but we have been too much busy with the end of the year. I hope w will be making a submission on 2017 :) Happy new year for you. Best regards. 2017-12-08 23:05 GMT-03:00 Noam Ross <notifications@github.com>:

…

Any update on this, @kenarab <https://github.com/kenarab>? — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#157 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACzA1v1a-BPE_UBJXZ7mh48Yh-DLAFOFks5s-er_gaJpZM4QYpu6> .

-- alejandro baranek @ken4rab <https://twitter.com/ken4rab> qbotics <http://qbotics.tumblr.com/> | surferinvaders <http://surferinvaders.tumblr.com> | algebraic-soundscapes <http://imaginary.org/content/algebraic-soundscapes> | surfer-shuffle <http://imaginary.org/program/surfer-shuffle>

[noamross]

Hi @kenarab! Just checking to see if you have a time frame for following up on this.

[kenarab]

Hello Noam: We are up to push, but couldn’t made the timeframe to concentrate on the release. We hope will do it in the next days. Best regards, Ale. Enviado desde el móvil El 22 feb. 2018, a la(s) 13:33, Noam Ross <notifications@github.com> escribió:

…

Hi @kenarab! Just checking to see if you have a time frame for following up on this. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or mute the thread.