[REVIEW]: overviewR - Easily Explore Your Data in R

[editorialbot]

Submitting author: @cosimameyer (Cosima Meyer)
Repository: https://github.com/cosimameyer/overviewR
Branch with paper.md (empty if default branch): master
Version: v0.0.12
Editor: @samhforbes
Reviewers: @drmowinckels, @milenamilena
Archive: 10.5281/zenodo.7097560

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/b161adf6c81cedb2bda1ae36b54c6ce0"><img src="https://joss.theoj.org/papers/b161adf6c81cedb2bda1ae36b54c6ce0/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/b161adf6c81cedb2bda1ae36b54c6ce0/status.svg)](https://joss.theoj.org/papers/b161adf6c81cedb2bda1ae36b54c6ce0)

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

@drmowinckels & @milenamilena, 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 @samhforbes 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 @drmowinckels

📝 Checklist for @milenamilena

[editorialbot]

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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (988.6 files/s, 218182.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            34           1727            470           9116
R                               25            226            581           1975
Markdown                         6            369              0           1349
Rmd                              4            319            857            429
CSS                              3             99             48            428
JavaScript                       4             64             34            266
YAML                             7             35              6            237
TeX                              1             11              0            102
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            85           2850           1997          13913
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1167

[editorialbot]

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[samhforbes]

Hi @drmowinckels, @milenamilena, please see the instructions at the top of the review thread.

Once you've generated your checklist you can use this as the basis for your review.
Generally speaking it's useful to post an overview here, but deal with individual points by opening issues on the target repository, and linking them here so we are all on the same page.
Feel free to direct any queries to me, but otherwise we look forward to the benefit of your expertise.

[drmowinckels]

Review checklist for @drmowinckels

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/cosimameyer/overviewR?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@cosimameyer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[milenamilena]

Review checklist for @milenamilena

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/cosimameyer/overviewR?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@cosimameyer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[cosimameyer]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[cosimameyer]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[cosimameyer]

@milenamilena @drmowinckels Many thanks for your feedback so far - I highly appreciate your time and energy going into it! I incorporated your suggested changes that we have received so far and updated the PDF.

[milenamilena]

I have completed my review, and I found this package very useful and holistic in giving an overview of data. The functions are very clear and well explained. The latex tables were beneficial, as the format is very clear. I also found very interesting the use of the Venn diagram and the ability to customise some gglots. I agree with the comments made by @drmowinckels and am happy to see that they were addressed. It is very promising to see that there are open issues in the repository, mainly for further enhancement. The whole paper is very explanatory, even for a naive R user.

[drmowinckels]

I have completed my review and am happy with the responses and changes made to the package and paper. The package functionality is well documented and covers something that has no real alternative in the R eco-system as I know it. Its clearly well-thought out and tested, and the implementation is great.

@samhforbes I believe both reviewers are happy with the package and paper status.

[samhforbes]

@editorialbot generate pdf

[xuanxu]

is there a way to include the footnote info somewhere?

Maybe adding it as a second affiliation for both authors?

[cosimameyer]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[cosimameyer]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[samhforbes]

Thanks @editorialbot
We are going to try again for real! Fingers crossed.

[editorialbot]

You are welcome

[cosimameyer]

Excellent suggestion, thanks @xuanxu.
I archived the new version at @samhforbes, the new DOI is 10.5281/zenodo.7097560 (https://doi.org/10.5281/zenodo.7097560). Can you update it?

[samhforbes]

@editorialbot set 10.5281/zenodo.7097560 as archive

[editorialbot]

Done! Archive is now 10.5281/zenodo.7097560

[samhforbes]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1080/09557571.2021.1980498 is OK
- 10.1093/jogss/ogac009 is OK
- 10.21105/joss.01509 is OK
- 10.32614/RJ-2019-033 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3542, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[cosimameyer]

This looks great 🚀 What a wonderful way to (possibly) finish a workday! :)

[kyleniemeyer]

Hi @cosimameyer, I just made a PR with a few minor edits to the paper, could you merge that? cosimameyer/overviewR#34

Then I can proceed with accepting the paper.

[cosimameyer]

Thanks, @kyleniemeyer - it's merged 😊

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04740 joss-papers#3543
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04740
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congratulations @cosimameyer on your article's publication in JOSS!

Many thanks to @drmowinckels and @milenamilena for reviewing this, and @samhforbes for editing.

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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reStructuredText:
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