Submission group 6: linregasm (R)

name: linregasm about: This package is built to contain functions to be able to quickly and easily test the linearity assumptions before preforming linear regression or multiple linear regression for a specified dataset.

Submitting Authors:

Yair Guterman (@gutermanyair)
Hatef Rahmani (@hatefr)
Andy Yang (@AndyYang80)

Repository: https://github.com/UBC-MDS/linregasm Version submitted: 1.0.0 Submission type: Standard Editor: TBD

Reviewers:

Steven Leung
Mahmood Rahman
Samuel Quist
Wai-Shan Yuen

Archive: TBD Version accepted: TBD

Package: linregasm
Title: Package for testing linear and multiple linear regression assumptions
Version: 0.0.0.9000
Authors@R: 
    c(person("Yair", "Guterman", ,"yairguterman1@gmail.com", role = c("aut", "cre")),
      person("Hatef ", "Rahmani", ,"hatef.rahmani.f@gmail.com"),
      person("Song ", "Yang", ,"sbayang@uwaterloo.ca"))
Description: This package is built to contain functions to be able to quickly and easily test the linearity assumptions befre preforming linear regression or multiple linear regression for a specified dataset. The package contains 3 functions one for checking multicolliniarity, one for checking constant variance and one for checking normality in the residuals.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.1
Suggests: 
    rmarkdown,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: 
    dplyr,
    car,
    ggplot2,
    tibble,
    knitr
VignetteBuilder: knitr

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
- [x] data extraction
- [ ] 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):

Our package extracts validity insights about linear regression assumptions from existing dataframes
Who is the target audience and what are scientific applications of this package?

We are catering this package towards data scientists, students, or working professionals who need to validate the validity of their linear regression models.
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 are no packages that accomplish the same functionality.
(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?
If you made a pre-submission inquiry, please paste the link to the corresponding issue, forum post, or other discussion, or @tag the editor you contacted.
Explain reasons for any pkgcheck items which your package is unable to pass.

Technical checks

Confirm each of the following by checking the box.

[x] I have read the guide for authors and rOpenSci packaging guide.

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.

Publication options

[x] Do you intend for this package to go on CRAN?
[ ] Do you intend for this package to go on Bioconductor?
[ ] Do you wish to submit an Applications Article about your package to Methods in Ecology and Evolution? If so:

MEE Options

- [ ] The package is novel and will be of interest to the broad readership of the journal. - [ ] The manuscript describing the package is no longer than 3000 words. - [ ] You intend to archive the code for the package in a long-term repository which meets the requirements of the journal (see [MEE's Policy on Publishing Code](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/journal-resources/policy-on-publishing-code.html)) - (*Scope: Do consider MEE's [Aims and Scope](http://besjournals.onlinelibrary.wiley.com/hub/journal/10.1111/(ISSN)2041-210X/aims-and-scope/read-full-aims-and-scope.html) for your manuscript. We make no guarantee that your manuscript will be within MEE scope.*) - (*Although not required, we strongly recommend having a full manuscript prepared when you submit here.*) - (*Please do not submit your package separately to Methods in Ecology and Evolution*)

Code of conduct

[x] I agree to abide by rOpenSci's Code of Conduct during the review process and in maintaining my package should it be accepted.

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: 47 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

It cannot yet be installed from "CRAN". I recommend removing that part of the installation instruction until it is ready;
The normality() example in the "Usage" section forgot to mention running the line library(linregasm) or be explicit with linregasm::normality(). I know it might be obvious but the "Usage" section should be self-sufficient. Also, there should be definitions of the dummy data frames and values for the examples to run. In fact, the examples in the vignettes are better than those in "Usage";
The examples in the "Usage" section should also show the optional arguments of p_threshold and threshold;
The README.md does mention about "contributing guidelines" but there is no standalone file. The closest thing I can find is the CODE_OF_CONDUCT.md (entitled "Contributor Covenant Code of Conduct"). But the document only talks about the general principles but NOT specific process of contributing (like creating a GitHub issue, or Pull Request, or contacting the authors via a certain mean);
For the multicollinearity() function, I suggest that the function proactively try to simulate the removal of the feature with the highest VIF and see what the VIFs of the subset of the features would look like;
The tests run with 0 errors and 0 warnings. Well done!
No codedev or ci-cd badges on README; and
Last but not least, the package is really useful for understanding the features before starting with linear regression. Well done.

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
[ ] 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:

[ ] 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

You may consider to publish your documentation on a website and link it from README so that other users can locate the documentation pages easier.
No URL and BugReports link find in DESCRIPTION file.
I am able to install your package by following the installation instruction, but I guess the installation from CRAN is not relevant.
Adding sample outputs in the usage and examples section can help others to understand the usage better
You may also consider to add the ci-cd and codecov badges on README page so that other users would know clearly about the project status.
The objective and functionalities of the packages are well-explained on the README page. Overall, I think it is a useful package and simple to use.

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: ~30 mins

[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

For the homoscedasticity function, returning a null list instead of just an error message might be a bit confusing. However I understand how hard it is to correctly assert that the parameters for that function are correct so perhaps this is not an option.
Tests all completed with no errors and the functions performed expectedly when I gave them a variety of parameters.
No CodeCov or R-CMD check badges on the readme, making it difficult to determine whether or not the code has had tests written for functionality from an outside perspective.
A rather minor issue but for all 3 functions, the default/optional parameters are not listed in the roxygen as optional or with default values.
Another small issue, there seems to be a typo in the Usage section of the README: "Test for Multicollinearity To test for homoscedasticity, use the..."
Apart from the things mentioned above I think the package looks great and will be helpful for anyone looking to learn more about regression models and assumptions with them.

Package Review

[x] As the reviewer I confirm that there are no conflicts of interest for me to review this work.

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:

[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

A link to the vignette can be shared with user by putting it in "about" section or read.me file
An evidence of code.cov anywhere in the front page could have been helpful.
This can be showcased along with CI implementation, license and code-coverage through batches.
An open issue is kept relating to license issue, which can be closed if resolved.
Excellent functionality and sufficient documentation of the package.

UBC-MDS / software-review-2022