Submission group 18: collinearityR (R)

name: collinearityR about: Easy code to detect collinearity issues

Submitting Author Name: Lisheng Mao Submitting Author Github Handle: Lisheng Mao @nickmao1994 Other Package Authors Github handles: Anahita Einolghozati @Anahita97, Chaoran Wnag @showcy, ,Katia Aristova @katerinkus Repository: https://github.com/UBC-MDS/collinearityR_tool Version submitted: TBD Submission type: Standard Editor: TBD Reviewers: Francis Victor @Vikiano, TZ Yan @ytz, Karanpreet Kaur @karanpreetkaur

Archive: TBD Version accepted: TBD Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: collinearityR
Title: Identify Multicollinearity Issues
Version: 0.0.0.9000
Authors@R: 
    c(person(given = "Anahita",
           family = "Einolghozati",
           role = c("aut", "cre"),
           email = "anahitaainy@gmail.com"),
    person(given = "Chaoran",
           family = "Wang",
           role = "aut"),
    person(given = "Katia",
           family = "Aristova",
           role = "aut"),
    person(given = "Lisheng",
           family = "Mao",
           role = "aut"))
Description: Identify multicollinearity issues by correlation, VIF, and visualizations.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: 
    tidyselect,
    stringr,
    purrr,
    rlang,
    ggplot2,
    dplyr,
    tidyr,
    tibble,
    car

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
- [x] 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):

This package automates the process of data cleaning and melting and generates heatmap and VIF bar plot.
Who is the target audience and what are scientific applications of this package?

Beginners who know statistics but have no or little experience in R.
Are there other R packages that accomplish the same thing? If so, how does yours differ or meet our criteria for best-in-category?
(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.

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[ ] 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:

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- [ ] 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: 1 hr

[ ] 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 example in corr_matrix, I think it will be great to include the output. I'm not sure why it is not rendering in the example. Perhaps you can try to be more explicit by calling output_corr_matrix[1] and output_corr_matrix[2] explicitly
Vignette is informative and simple to follow 👍
Similar to the comment for the Python package, I find that showing a simple example of output from the functions in README.md will help me understand what each function offers
I wasn't sure which parameters were optionals for some functions. I think the approach writing (optional) at the front in col_identify is good
I wasn't sure what kind of string is needed for color_neg and color_pos in corr_heatmap. An example or further details would be very helpful.

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: 1 hour

[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

Good to notice that you have added badges for code coverage and ci-cd in README and also you have improved your code coverage to 100%. Good work guys.
In README, you have included the dependencies of your package in the R ecosystem section. I think it would be good to have separate section for Motivation/Our place in Python ecosystem section and Dependencies.
Your docstrings are great, however the functions could probably use a few more comments to increase readability. Not a big issue but would be nicer to read to fully understand what's going on.
Your LICENSE file misses all contributor's name and also DESCRIPTION could also have email address of all authors.
For function vif_bar_plot, do you feel to have a default threshold value. Looking at beginner's perspective, many times people use functions without knowing purpose of threshold and having a default threshold could set a context and gives them opportunity to play with it according to their need.
In Usage, you can clearly specify link to documentation (like Please find the detailed documentation in the vignette) instead of This to give clarity to readers.
Also, It would be good to add LICENSE and Contributing section in README as the CONTRIBUTING.md file lives in .github and thus readers might not see it directly. Thus, good to include a section in README for it's reference.

Overall, this is a useful and much needed package in R and I enjoyed reviewing it. 👍

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: 1 hour

[ ] 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 was able to follow the detailed installation instruction, and successfully installed your package with no single issue.
The usage instructions on the repo was neatly done and very easy to follow. I got your package to function as designed on my computer.
My favourite part of your package is how clear and unambiguous your functions documentation are.
An example output would have gone a long way in even showing more democstration of what your package does if shown. My suggestion is that you show this in the homepage i.e the readme portion of your repo.
Overall, great package. Kudos to the team 👍

UBC-MDS / software-review-2022