Submission Group 23: coordgeomr (R)

Submitting Author Name: Arlin Cherian, Jordan Casoli, Nico Van den Hooff, Zheren Xu Submitting Author Github Handle: @arlincherian, @jcasoli, @nicovandenhooff, @ZherenXu Repository: https://github.com/UBC-MDS/CoordGeomR Version submitted: v1.0.0 Submission type: Standard Editor: TBD Reviewers: Vera Cui, Jasmine ORTEGA, Mel Liow, Anahita Einolghozati

Archive: TBD Version accepted: TBD Language: en

DESCRIPTION:

Package: CoordGeomR
Title: A simple coordinate geometry helper package
Version: 0.0.0.9000
Authors@R: 
    c(person(given = "Arlin",
           family = "Cherian",
           role = c("aut", "cre"),
           email = "arlin.cherian@ubc.ca"),
    person(given = "Jordan",
           family = "Casoli",
           role = c("aut"),
           email = "casolijordan@gmail.com"),
    person(given = "Nico",
           family = "Van den Hoodd",
           role = c("aut"),
           email = "nicovandenhooff@gmail.com"),
    person(given = "Zheren",
           family = "Xu",
           role = c("aut"),
           email = "xuzheren1998@gmail.com"))
Description: This starter package allows users to perform various geometric operations like calculate distance between them two parallel lines, distance between two n dimensional vectors, intersection of lines in 3-Dimensional space and so on. 
License: MIT + file LICENSE
Encoding: UTF-8
Depends: pracma
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests: 
    testthat (>= 3.0.0),
    covr
Config/testthat/edition: 3

Scope

Please indicate which category or categories from our package fit policies this package falls under: (Please check an appropriate box below. If you are unsure, we suggest you make a pre-submission inquiry.):
- [ ] data retrieval
- [ ] data extraction
- [x] data munging
- [ ] data deposition
- [ ] workflow automation
- [ ] version control
- [ ] citation management and bibliometrics
- [ ] scientific software wrappers
- [ ] field and lab reproducibility tools
- [ ] database software bindings
- [ ] geospatial data
- [ ] text analysis
Explain how and why the package falls under these categories (briefly, 1-2 sentences): coordgeomr is a simple coordinate geometry helper package. It allows users to perform various geometric operations
Who is the target audience and what are scientific applications of this package? Data analysts, statisticians or any other R users who need to do simple geometry calculations.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category? There is an existing package called LearnGeom that executes similar functions. For example, the package has functions like DistanceLines that computes the distance between two lines and IntersectLines which finds the intersection of two lines. The intention for coordgeomr is to be a light and beginner-friendly R library for basic geometry manipulation.
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Technical checks

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This package:

[x] does not violate the Terms of Service of any service it interacts with.
[x] has a CRAN and OSI accepted license.
[x] contains a README with instructions for installing the development version.
[x] includes documentation with examples for all functions, created with roxygen2.
[x] contains a vignette with examples of its essential functions and uses.
[x] has a test suite.
[x] has continuous integration, including reporting of test coverage using services such as Travis CI, Coveralls and/or CodeCov.

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Code of conduct

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Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
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Documentation

The package includes all the following forms of documentation:

[X] A statement of need: clearly stating problems the software is designed to solve and its target audience in README
[X] Installation instructions: for the development version of package and any non-standard dependencies in README
[X] Vignette(s): demonstrating major functionality that runs successfully locally
[X] Function Documentation: for all exported functions
[X] Examples: (that run successfully locally) for all exported functions
[X] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[X] Installation: Installation succeeds as documented.
[X] Functionality: Any functional claims of the software been confirmed.
[X] Performance: Any performance claims of the software been confirmed.
[X] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
[X] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 45 minutes

[X] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

I have to say it's great work, and I really enjoyed having this chance to play around. The project is well organized and everything is clearly stated and documented.
There is no link of the knitted documentation which might be added to show user how to use more directly.
More detail can be added to the Usage part where only one function is listed.
The README misses the citation section since the whole package is not built from scratch, like that pracma can be referred to.
I think it's necessary to add dependencies in READEME to show users required packages.

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
[X] As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[X] A statement of need: clearly stating problems the software is designed to solve and its target audience in README
[X] Installation instructions: for the development version of package and any non-standard dependencies in README
[X] Vignette(s): demonstrating major functionality that runs successfully locally
[X] Function Documentation: for all exported functions
[X] Examples: (that run successfully locally) for all exported functions
[X] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[X] Installation: Installation succeeds as documented.
[X] Functionality: Any functional claims of the software been confirmed.
[X] Performance: Any performance claims of the software been confirmed.
[X] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
[X] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 1hr

[X] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

Really well written package with clear and detailed documentation and neat code.
Great work on the tests having 100% coverage. They are also very thorough and well commented. I feel like it would be very easy to contribute and add to your unit tests.
I would just double check that the comments align to what the test does - e.g the comment should say "float" rather than "integer"
```
# ------ tests is_orthogonal with integer input ------
test_that("Error in is_orthogonal for float input", { ...}
```
Similar to the above comment, the Example section in the ReadMe is lacking a little with only one function demonstrated.
You might still be working on hosting the Vignette through github pages but it's not currently link on the Readme
Overall, great work!!

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[x] A statement of need: clearly stating problems the software is designed to solve and its target audience in README
[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[ ] Vignette(s): demonstrating major functionality that runs successfully locally
[x] Function Documentation: for all exported functions
[x] Examples: (that run successfully locally) for all exported functions
[x] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 1hours

[x] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

The "docs" folder is missing from the main repo and _pkgdown.yml is empty as well -- this is probably the source of the missing vignette mentioned by other commentors.
There are specifics from Milestone 1 that are missing from the README that would really be great enhancements to the main page of the repo (ie. how this package fits in with the rest of the R ecosystem, etc) 3 . The documentation for dist_pll_lines_2d has a mistake under value/example
```
Value
d, A numerical value for distance between the two parallel lines
```

dist_pll_lines_2d(-4, 11, 23) d <- "2.9104"


As is, I thought this was some input I needed to create a var `d <-` to make the function work. It was a little confusing as a new user to the function. 
4.  I think the R documentation for `is_intersection_3d` description is too long. Just the first sentence of  the description would be sufficient -- "Determines whether two infinite lines intersect in 3-dimensional space." I don't think a full paragraph is necessary. 
5.  There are 17 active branches on the main repo and some of them seem repetitive and/or have now defunct purposes.  For example,  `feat_is_intersection_3d` and `feat_is_intersection`. I think for contributing purposes, it would be cut down on the number of branches. 

Overall, this was an extremely well done package and I'm impressed by the quality achieved in a few short weeks. I apologize for the nit-picky comments - it was hard to find things to comment on! So don't take these critiques too harshly. 😆 Great job!

Package Review

Please check off boxes as applicable, and elaborate in comments below. Your review is not limited to these topics, as described in the reviewer guide

Briefly describe any working relationship you have (had) with the package authors.
[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (if you are unsure whether you are in conflict, please speak to your editor before starting your review).

Documentation

The package includes all the following forms of documentation:

[x] A statement of need: clearly stating problems the software is designed to solve and its target audience in README
[x] Installation instructions: for the development version of package and any non-standard dependencies in README
[x] Vignette(s): demonstrating major functionality that runs successfully locally
[ ] Function Documentation: for all exported functions
[x] Examples: (that run successfully locally) for all exported functions
[x] Community guidelines: including contribution guidelines in the README or CONTRIBUTING, and DESCRIPTION with URL, BugReports and Maintainer (which may be autogenerated via Authors@R).

Functionality

[x] Installation: Installation succeeds as documented.
[x] Functionality: Any functional claims of the software been confirmed.
[x] Performance: Any performance claims of the software been confirmed.
[x] Automated tests: Unit tests cover essential functions of the package and a reasonable range of inputs and conditions. All tests pass on the local machine.
[x] Packaging guidelines: The package conforms to the rOpenSci packaging guidelines.

Estimated hours spent reviewing: 1

[x] Should the author(s) deem it appropriate, I agree to be acknowledged as a package reviewer ("rev" role) in the package DESCRIPTION file.

Review Comments

Great work! Here are some minor points to consider.

I think choosing a package name that would follow a similar format for both R and Python packages would have been helpful. Currently, the R package is named CoordGeomR, whereas the Python package is named coordgeompy. I personally prefer the R package name, since the capital letters helps with easier readability.
I think since the functions in this package recreate functions that already exist in other packages, it would have been good to explain why a user might want to use CoordGeomR over other packages in the motivation section.
As mentioned, it seems like the rendered vignette does not show up in the repo.
I really liked the testing of the package. I think different test functions for different purposes is definitely organized very well and is easy to read.
Just a very minor comment about the testing comments, for is_orthogonal tests, the comments for two of test functions repeat "tests is_orthogonal with integer input", but it seems like the last test function is actually testing float input. Also, the inputs test for this function will just throw an error of "Invalid inputs". It could be helpful to provide a more helpful error message.
Currently the example, includes the usage of only one of the functions. It would be helpful to include examples of other functions in the package.
Very detailed docstrings for the functions that help the user understand what each of them do, and in particular, I found the defensive programming to be very impressive.

UBC-MDS / software-review-2022