Group 5: EDAhelperR (R)

name: EDAhelperR about: R package

Submitting Author Name: Name Submitting Author Github Handle: !--author1-->@[stevenleung2018](@stevenleung2018)<!--end-author1-- Other Package Authors Github handles: (comma separated, delete if none) @suuuuperNOVA, @jennifer-hoang, @Rowansiv Repository: https://github.com/UBC-MDS/EDAhelperR Version submitted: Submission type: Standard Editor: TBD Reviewers: Irene Yan, Macy Chan, Yike Shi, Chaoran Wang

Archive: TBD Version accepted: TBD Language: en

Paste the full DESCRIPTION file inside a code block below:

Package: EDAhelperR
Title: Tools to make EDA easier!
Version: 1.0.0
Authors@R: 
    c(person(given = "Vera",
             family = "Cui",
             email = "jinglu_cui@163.com",
             role = c("aut", "cre"),
             comment = c(ORCID = "0000-0002-7873-312X")),
      person(given = "Steven",
             family = "Leung",
             email = "example@email.com",
             role = c("aut", "ctb"),
             comment = c(ORCID = "ORCID")),
      person(given = "Rowan",
             family = "Sivanandam",
             email = "example@email.com",
             role = c("aut", "ctb"),
             comment = c(ORCID = "ORCID")),
      person(given = "Jennifer",
             family = "Hoang",
             email = "example@email.com",
             role = c("aut", "ctb"),
             comment = c(ORCID = "ORCID")))
Description: This package is aimed at making the EDA process more effective within following functions: 1. To clean the data and replace missing values by using the method preferred; 2. To provide the description of the data such as the distribution of each column of the data, 3. To give the correlation plot between different columns and omit the pairs that are not significantly correlated; 4. To combine the plots and make them suitable for the report.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests: 
    testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: 
    dplyr,
    stats,
    readr,
    ggplot2,
    tidyr,
    rlang,
    GGally,
    modest

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.):
- [x] data retrieval
- [x] 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 is a package for EDA (Exploratory Data Analysis). It therefore has elements of data retrieval, extraction, munging and some data visualization.

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

It is targeted for any data scientist who does Explanatory Data Analysis.

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

Surely, EDA is not a new topic to data scientists. There are quite a few packages doing similar work on CRAN. However, most of them only include limited functions like just providing descriptive statistics. Our proposal is more of a one-in-all toolkit for EDA. Below is a list of sister-projects.

brinton : A Graphical EDA Tool correlationfunnel : Speed Up Exploratory Data Analysis (EDA) with the Correlation Funnel ezEDA : Task Oriented Interface for Exploratory Data Analysis

These packages either focus a lot on graphical EDA or generating a large chart or report with a single large function. With EDAhelperR, we try to offer short, simple function calls which can be used in reports.

There are a few Python packages which also work on EDA, but they position themselves differently compared to EDAhelper. Some packages do only 1 function. Some packages provide functions which almost generate a comprehensive report. We want to provide a packages with individual function calls which can be used in different parts of a report.

(If applicable) Does your package comply with our guidance around Ethics, Data Privacy and Human Subjects Research?

Not applicable.

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.
[ ] contains a vignette with examples of its essential functions and uses.
[x] has a test suite.
[ ] 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

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:

[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

Feedback:

Tested all the functions and did testing on local, all ran without any issue. Good job!
For Vignette documentation, I found function discriptions and articles are pretty similar. It would be nice if the article can be presented in a story form, so that it can demonstrate (1) how this package can benefit a user in a project or (2) How much time can be saved.
One more point for Vignette, it would be nice to include some function limitations, what can/ cannot do.

Related to previous point, I tested column_stats() , seem it doesn't handle NA well.

file_path = "https://raw.githubusercontent.com/pandas-dev/pandas/main/doc/data/titanic.csv"
df = preprocess(file_path)
column_stats(df, c('Survived', 'Age'))

Error in quantile.default(data[[column]], 0.25) : 
missing values and NaN's not allowed if 'na.rm' is FALSE

Also, when I look up help in R-studio, the roxygen doesn't come up. Not sure if it's just my local issue.

Overall, I enjoy testing the package and I can see how it can benefit for EDA. =]

Also, when I look up help in R-studio, the roxygen doesn't come up. Not sure if it's just my local issue.

Hi Macy, thanks for taking time in a detailed review!

I would like to follow up on the HTML page not found issued at RStudio under the "Help" tab. I am not able to reproduce the issue. Would you provide some steps on how it can be reproduced?

After installation, I just go to help tab and search the function name

After installation, I just go to help tab and search the function name

Did u load the package? 'library(EDAhelperR)'

I didn't, but I restarted the R studio and it works now =]

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: half an 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

Great job team! Package successfully installed and all function are running smoothly on my end.

Here are a few things that I came up with:

When I tested the column_stat() function with wrong input:

I thought the error message would be column not exists in the data frame or something like that? This error message is not informative from my point of view.
It would be nice to use the same dataframe to illustrate the function in the usage of README file, also include the desired output(screenshot, etc), which helps user better understand the function.

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:

[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

Similar to your python package, your function EDAhelper only has one function preprocess and you have all other functions with separate files which is confused. It might be better to be consistent, either all named with function name or put all functions into the EDAhelper file.
It is better to use comment line to explain your usage example.
It is better to put readr::readr_example part inside your function instead of asking users use your function in this way. It is not intuitive enough.
Hmm, please ignore my last comment because your this example does not work: preprocess(readr::readr_example("mtcars.csv”)) actually… T.T It. Should be preprocess("mtcars.csv")
For column_stats function, it fails when the column names are a string with spaces. You might need to handle this situation, either process it or return errors. Currently, the error is with these lines: error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
For numeric_plots, it might be better to add columns attributes to be consistent as your other three 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: 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

I find the output of column_stats() function a bit disorienting: the correlation and covariance matrices do not have appropriate titles for differentiation.

Some error messages are not informative and do not provide guidance on how to proceed. For example:

column_stats(mtcars, c("mpg", "cyl"))
Error in dimnames(x) <- dn : 
length of 'dimnames' [2] not equal to array extent
In addition: Warning message:
In rbind(summary_stats, new_row) :
number of columns of result is not a multiple of vector length (arg 2)

It would be nice if the columns can be selected to produce the plots in the numeric_plots() function.
It would be better to include the output plots in your usage section in README
Overall, this package looks pretty useful for EDA and I will be sure to incorporate it in my project!

UBC-MDS / software-review-2022