Submission Group 7: reasyeda (R)

Name: reasyeda About: An R package that aims to perform basic exploratory data analysis on raw data.

Submitting Author Name: Sukhleen Kaur Submitting Author Github Handle: @sukhleen999 Other Package Authors Github handles: @jamesktkim, @khbunyan, @Luming-ubc Repository: reasyeda Version submitted: 1.0.0 Submission type: Standard Editor: TBD Archive: TBD Version accepted: TBD Language: en Reviewers:

Manju Neervaram Abhinandana Kumar
Steven Lio
Wenxin Xiang
Nikita Shymberg
DESCRIPTION file:

Package: reasyeda
Title: Make Exploratory Data Analysis Easier
Version: 0.0.0.9000
Authors@R: 
    person(given = "James",
           family = "Kim",
           role = c("aut", "cre"),
           email = "first.last@example.com",
           comment = c(ORCID = "YOUR-ORCID-ID"))
    person(given = "Kristin",
           family = "Bunyan",
           role = c("aut", "cre"),
           email = "first.last@example.com",
           comment = c(ORCID = "YOUR-ORCID-ID"))
    person(given = "Sukhleen",
           family = "Kaur",
           role = c("aut", "cre"),
           email = "first.last@example.com",
           comment = c(ORCID = "YOUR-ORCID-ID"))
    person(given = "Luming",
           family = "Yang",
           role = c("aut", "cre"),
           email = "lumingyang.ut@gmail.com",
           comment = c(ORCID = "YOUR-ORCID-ID"))
Description: What the package does (one paragraph).
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests: 
    covr,
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: 
    ggplot2,
    dplyr,
    GGally,
    tidyr,
    palmerpenguins,
    purrr,
    forcats,
    cowplot,
    stats,
    pastecs,
    readr,
    tibble,
    Hmisc

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):

This package is designed to offer simple functions that make preliminary exploratory data analysis easier by performing data wrangling and data visualization.

Who is the target audience and what are scientific applications of this package?

Any individual who faces the need to perform data analysis of any complexity can leverage this package to kick-start their work.

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

The package that closely resembles our package is DataExplorer. However, the functions in reasyeda enable the users to customize them as appropriate.

(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

[ ] 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 for reasyeda

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.

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 the 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
[ ] 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 have been confirmed.
[X] Performance: Any performance claims of the software have been confirmed.
[ ] 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 reasyeda 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

Excellent package for the EDA process. Functions are easy to use and it is fast too. Can add more functions to the process to enrich the package like imputation methods, PCA, regrouping categorical variables (small groups) etc.

birds_eye_view() function from the example is not runnable. An issue is raised here.
clean_up() user should know the output of the function if it overwrites the original data or a new object is needed to be created.
summary_suggestions() output is not intuitive as there are 3 tables output and not clear what the metrics are.
Example can be made the more fluid process and showcase the output from each function so the user will know what to expect.
Functions should be more flexible in dealing with bigger data set (e.g. 1000 columns). Since the user can't control how many plots it will generate.

title: "review" output: rmarkdown::md_document: pandoc_args: [ "--wrap=none" ]

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
[ ] 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.
[ ] 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 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

Overall: great!

I'm afraid I couldn't find any vignettes - maybe I'm reviewing too early.
The type of the var_list parameter in the birds_eye_view is not clear - I guess it should be a character vector?
Really minor: I noticed that there are no spaces around the n parameter in the close_up function definition.
I love the extensive tests for the two visualization functions!
I wish the example in the README also included the outputs of the functions.

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

It's a very useful package for preliminary exploratory data analysis. It's so amazing that the test coverage is 99%.

I really like that the link for document is included in the readme file that it's very easy for users to find.
It's better to include code maintainer's email information in the Contributing.md file. People who are interested in contributing need to know who to contact.
For the heatmap of the function birds_eye_view, part of the text overlapped one another. Maybe it's better to format the chart or the size of text.
It may be better if the docstring of functions could be displayed somewhere in the documents or readme. Currently I can only find it in the R.script.
It's better to show example output in the readme file.
For the function of summary_suggestions, I find it a little bit hard to understand the function of threshold in the function. Maybe it's better to explain in the docstring about what will be returned if the unique values is below or above the threshold, so that users can know what to expect.

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: 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

A very useful package to perform EDA. Good job, Team!

The documentation in github pages is very good and detailed.
The examples in README could include more details like a brief description, what arguments it takes followed by code chunk.
I was able to reproduce the results using the example code given in R studio and Jupyter notebook.
There is excellent code coverage. The tests and check passed.
nice to have: An option to choose/view only a particular plot or plots, say only histograms from all the plots generated

UBC-MDS / software-review-2022