[REVIEW]: datawizard: An R Package for Easy Data Preparation and Statistical Transformations

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@IndrajeetPatil@osorensen<!--end-editor-- Reviewers: @tomfaulkenberry, @garretrc Archive: 10.5281/zenodo.7143971

Status

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Markdown: [![status](https://joss.theoj.org/papers/e091e4c73d855e87d0d774eafed63964/status.svg)](https://joss.theoj.org/papers/e091e4c73d855e87d0d774eafed63964)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@tomfaulkenberry & @garretrc, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @garretrc

📝 Checklist for @tomfaulkenberry

editorialbot commented 2 years ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (706.1 files/s, 114435.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                              111           2566           4339          10862
Markdown                        25            464              0           1816
XML                              1              0            129           1787
Rmd                              4            435            788            496
TeX                              2             47              0            272
YAML                             7             56             17            237
-------------------------------------------------------------------------------
SUM:                           150           3568           5273          15470
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1417

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.02815 is OK
- 10.21105/joss.02445 is OK
- 10.21105/joss.03393 is OK
- 10.21105/joss.03139 is OK
- 10.21105/joss.01412 is OK
- 10.21105/joss.02306 is OK
- 10.21105/joss.03167 is OK
- 10.21105/joss.01541 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

garretrc commented 2 years ago

Review checklist for @garretrc

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/easystats/datawizard?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@IndrajeetPatil) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

osorensen commented 2 years ago

:wave: @tomfaulkenberry, @garretrc, could you please update us on how it's going with your reviews?

tomfaulkenberry commented 2 years ago

Should have it done today! I'm sorry for my delay...our semester got started right at the same time the review period got started. I appreciate the reminder :)

tomfaulkenberry commented 2 years ago

Review checklist for @tomfaulkenberry

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/easystats/datawizard?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@IndrajeetPatil) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

garretrc commented 2 years ago

thanks for the reminder, I'll start taking a look at the repo and docs today but may not be able to test functionality until next week

IndrajeetPatil commented 2 years ago

Version: 0.5.0

@osorensen We needed to make a new CRAN release. Therefore, can you please bump the version to 0.6.0? Thanks.

osorensen commented 2 years ago

@IndrajeetPatil, we set the final version once the paper is ready for acceptance, so no need to bump the version right now.

osorensen commented 2 years ago

But I can do it anyway:

osorensen commented 2 years ago

@editorialbot set 0.6.0 as version

editorialbot commented 2 years ago

Done! version is now 0.6.0

osorensen commented 2 years ago

👋 @tomfaulkenberry, @garretrc, could you please update us on how it's going with your reviews?

Feel free to add comments to your reviews in this thread, or to open issues in the source repository

garretrc commented 2 years ago

I've had the chance to incoporate many of the datawizard functions into my own workflow to test the functionality, I'll wrap up checking some of the remaining functions that I haven't been able to test today.

This package has a lot of useful functions even for experienced R users, so I'm also thinking about ways this package could best communicate that.

garretrc commented 2 years ago

Review finished. Everything I've tested returns the correct results and runs quickly. A couple comments:

I don't think the readme highlights the benefits of datawizard for an experienced R user (yes, a lot of the functions are quick to code up on your own, but you might save 5-10 minutes/a trip to stack overflow by using some datawizard "magic"). However, the easystats ecosystem page addresses this concern a bit, and the datawizard readme seems very detailed already. If I think of a better way to highlight this I'll raise an issue in the repo.
When using some of the functions, it's not clear from the tooltip in RStudio what the arguments should be. For example, when I use rescale(), center(), slide(), and others, only the x argument is included in the tooltip. So, when using the package I found myself needing to consult the help documentation in cases where I was expecting to just glance at the tooltip. My understanding is that these functions have different arguments for different data types and different operations, so the second argument will change for different use cases. The flexibility of each function to work with different data types without needing something like dplyr/data.table/base R data.frame manipulation seems more important to the package's mission than the tooltips, but just wanted to share this experience as a user.

The above points are small nitpicks, but I think the selection of functions in the package provides an accessible route to many common data manipulation tasks for new R users. For experienced R users who have previously coded the included operations on their own/through tidyverse or other packages, it seems just as fast to learn a new datawizard function than to look up/code up an equivalent solution. The datawizard functions are well-curated toward tasks that are annoying to remember/implement, so I believe they will be easier to recall and quicker to access than equivalent solutions from more general packages.

osorensen commented 2 years ago

Thanks a lot for your review @garretrc!

IndrajeetPatil commented 2 years ago

Dear @garretrc,

Thanks a lot for your wonderful assessment of {datawizard}. We are delighted to hear that you found the package useful, and think that it is equally accessible and useful for both naive and advanced R users.

I will respond to your nitpicks point-by-point.

You are absolutely right that we could be doing a better job of outlining functionality offered by the package. I have created an issue to remind us (https://github.com/easystats/datawizard/issues/271). Of course, if you think of some concrete suggestions, feel free to either comment on that issue or create a new issue.
Unfortunately, this is something that is beyond our control, and is a result of RStudio IDE works.

In this video, I demonstrate how, depending on the supplied argument, if you hit tab, the IDE will provide the accurate argument list. But, if put the cursor on the function name and hit tab, it always displays the same tooltip, irrespective of which S3 method is dispatched.

https://user-images.githubusercontent.com/11330453/192577004-8f343857-d432-4ba3-be2a-37ac8a02a529.mov

Thanks again for your review, and let us know if you have any other comments or suggestions.

garretrc commented 2 years ago

@IndrajeetPatil I'll leave a comment on that issue if I think of anything!

I didn't know you could supply the first argument like that to change the tooltip, it definitely improves the experience. Not really in your control to make sure a user inputs the first argument before pressing tab.

osorensen commented 2 years ago

@tomfaulkenberry could you please update us on how it's going with your review?

tomfaulkenberry commented 2 years ago

Sorry for the delay, @IndrajeetPatil! I have checked off everything in my review, and I'm happy to report that it works as it should. This is a really nice package...I particularly like the intuitive nature of the long <--> wide transformations, among many other things.

IndrajeetPatil commented 2 years ago

Thank you so much for the quick response, @tomfaulkenberry!

We are glad to hear that you find the functionality useful and intuitive :)

IndrajeetPatil commented 2 years ago

@osorensen What's the next step here?

osorensen commented 2 years ago

Thanks @tomfaulkenberry!

osorensen commented 2 years ago

@IndrajeetPatil, I will now read through the paper a final time and let you know if I have any suggested changes.

In the meantime, could you

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

osorensen commented 2 years ago

@editorialbot check references

osorensen commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.02815 is OK
- 10.21105/joss.02445 is OK
- 10.21105/joss.03393 is OK
- 10.21105/joss.03139 is OK
- 10.21105/joss.01412 is OK
- 10.21105/joss.02306 is OK
- 10.21105/joss.03167 is OK
- 10.21105/joss.01541 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

IndrajeetPatil commented 2 years ago

@osorensen Thanks for the checklist.

I have taken all the necessary steps here:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

I have created a tagged release for {datawizard}. Release version is: 0.6.2.

The DOI for the archived version on Zenodo is: 10.5281/zenodo.7143971

osorensen commented 2 years ago

@editorialbot set 10.5281/zenodo.714 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.714

osorensen commented 2 years ago

@editorialbot set 0.6.2 as version

editorialbot commented 2 years ago

Done! version is now 0.6.2

osorensen commented 2 years ago

Thanks @IndrajeetPatil. As you see, I've added a few editorial comments in the source repository. Please let me know when they have been resolved, and I can then move forward with accepting the submission.

IndrajeetPatil commented 2 years ago

Thanks for your careful read and helpful editorial suggestions on the paper, @osorensen! I have addressed all of them.

Let me know if you want me to make any other changes.

osorensen commented 2 years ago

@editorialbot generate pdf

osorensen commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.02815 is OK
- 10.21105/joss.02445 is OK
- 10.21105/joss.03393 is OK
- 10.21105/joss.03139 is OK
- 10.21105/joss.01412 is OK
- 10.21105/joss.02306 is OK
- 10.21105/joss.03167 is OK
- 10.21105/joss.01541 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.21105/joss.02815 is OK
- 10.21105/joss.02445 is OK
- 10.21105/joss.03393 is OK
- 10.21105/joss.03139 is OK
- 10.21105/joss.01412 is OK
- 10.21105/joss.02306 is OK
- 10.21105/joss.03167 is OK
- 10.21105/joss.01541 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 2 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3578, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

IndrajeetPatil commented 2 years ago

Check final proof

@osorensen I have checked the final proofs and everything looks good to me.

Let me know if there is anything else that I need to do. Thanks.

arfon commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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