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[REVIEW]: statsExpressions: R Package for Tidy Dataframes and Expressions with Statistical Details #3236

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whedon opened this issue May 3, 2021 · 63 comments
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@whedon
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whedon commented May 3, 2021

Submitting author: @IndrajeetPatil (Indrajeet Patil)
Repository: https://github.com/IndrajeetPatil/statsExpressions
Version: v1.0.1
Editor: @mikldk
Reviewer: @humanfactors, @tomfaulkenberry
Archive: 10.5281/zenodo.4773886

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0990e4123e0db077cf63ae9ebfa82e99"><img src="https://joss.theoj.org/papers/0990e4123e0db077cf63ae9ebfa82e99/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0990e4123e0db077cf63ae9ebfa82e99/status.svg)](https://joss.theoj.org/papers/0990e4123e0db077cf63ae9ebfa82e99)

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

@humanfactors & @tomfaulkenberry, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

Review checklist for @humanfactors

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@IndrajeetPatil) 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

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 and who the target audience is?
  • 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?

Review checklist for @tomfaulkenberry

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@IndrajeetPatil) 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

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 and who the target audience is?
  • 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?
@whedon
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whedon commented May 3, 2021

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @humanfactors, @tomfaulkenberry it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

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

@whedon generate pdf

@whedon
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whedon commented May 3, 2021

Failed to discover a Statement of need section in paper

@whedon
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whedon commented May 3, 2021

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.15 s (488.3 files/s, 79147.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               34            623           1377           4260
Markdown                        10            470              0           1602
Rmd                              4            324            702            609
XML                              1              0              2            441
YAML                            11             82              7            417
JSON                             1              0              0            398
TeX                              1             27              0            144
CSS                              1              3              0             13
SVG                              8              0              0              8
-------------------------------------------------------------------------------
SUM:                            71           1529           2088           7892
-------------------------------------------------------------------------------


Statistical information for the repository '19ce76c2bcaf18c91390b7b0' was
gathered on 2021/05/03.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Indrajeet Patil                 18           704            704          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments

@whedon
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whedon commented May 3, 2021

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

@mikldk
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mikldk commented May 3, 2021

@humanfactors, @tomfaulkenberry: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

@IndrajeetPatil Please note the error above "Failed to discover a Statement of need section in paper".

@whedon
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whedon commented May 3, 2021

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
- 10.5281/zenodo.3952174 is OK
- 10.21105/joss.01412 is OK
- 10.21105/joss.02306 is OK
- 10.5281/zenodo.2074621 is OK
- 10.21105/joss.01541 is OK
- 10.21105/joss.01686 is OK

MISSING DOIs

- 10.3758/s13428-019-01246-w may be a valid DOI for title: Robust Statistical Methods in R Using the WRS2 Package
- 10.31234/osf.io/yqxfr may be a valid DOI for title: The JASP guidelines for conducting and reporting a Bayesian analysis
- 10.32614/rj-2016-001 may be a valid DOI for title: metaplus: An R Package for the Analysis of Robust Meta-Analysis and Meta-Regression

INVALID DOIs

- None

@IndrajeetPatil
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@IndrajeetPatil Please note the error above "Failed to discover a Statement of need section in paper".

@mikldk Thanks, I have renamed the relevant section.

I have also added a sentence about how the software differs from broom, like you had asked:

https://github.com/IndrajeetPatil/statsExpressions/blob/7690a2587a2d856cf970002808da2a0bf13d8982/paper/paper.Rmd#L117-L120

@IndrajeetPatil
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@whedon generate pdf

@whedon
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whedon commented May 3, 2021

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

@IndrajeetPatil
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@whedon generate pdf

@whedon
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whedon commented May 3, 2021

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

@IndrajeetPatil
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@mikldk I am guessing this issue has been unintentionally tagged as waitlisted?

Screenshot 2021-05-03 at 14 54 18

@humanfactors
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I noticed that v 1.0.1 has been released since the package was submitted, should this be target for code review, and/or should the whedon version be updated?

@mikldk mikldk removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label May 4, 2021
@mikldk
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mikldk commented May 4, 2021

I noticed that v 1.0.1 has been released since the package was submitted, should this be target for code review, and/or should the whedon version be updated?

@IndrajeetPatil?

@IndrajeetPatil
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I noticed that v 1.0.1 has been released since the package was submitted, should this be target for code review, and/or should the whedon version be updated?

@humanfactors Thanks for pointing that out! Yes, it was a minor release to fix some issues.

The whedon version should be updated, but I don't know how to do it.

@mikldk
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mikldk commented May 4, 2021

@whedon set v1.0.1 as version

@whedon
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whedon commented May 4, 2021

OK. v1.0.1 is the version.

@IndrajeetPatil
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Thanks!

@IndrajeetPatil

This comment has been minimized.

@IndrajeetPatil
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@whedon generate pdf

@whedon
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whedon commented May 19, 2021

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

@IndrajeetPatil
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IndrajeetPatil commented May 19, 2021

@mikldk Thanks for providing the checklist.

  • I have done final proofreading and the language and style are OK.
  • I have checked the generated whedon PDF proofs, and it looks good.
  • There is already a release on GitHub with the version related to the paper
  • I have created a Zenodo-archive of this release and edited/checked the meta-data.
    I confirm that the GitHub release as well as the Zenodo-archive are the correct package versions and in the state that should be published.

The doi is 10.5281/zenodo.4773886.

Please let me know if you need any other details from my end. :)

@mikldk
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mikldk commented May 20, 2021

@whedon set 10.5281/zenodo.4773886 as archive

@whedon
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whedon commented May 20, 2021

OK. 10.5281/zenodo.4773886 is the archive.

@mikldk
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mikldk commented May 20, 2021

@whedon generate pdf

@whedon
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whedon commented May 20, 2021

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

@mikldk
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mikldk commented May 20, 2021

@IndrajeetPatil:

  • Please make the title at Zenodo the same as the paper's.
  • There is some confusing about the version: Zenodo has a 1.1.0 prior to this 1.0.1 -- this is not standard; can you please fix it.

@IndrajeetPatil
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IndrajeetPatil commented May 20, 2021

@mikldk

Thanks for pointing out these inconsistencies:

Please make the title at Zenodo the same as the paper's.

Done! The new title is the same as the paper
https://zenodo.org/record/4773886#.YKZOk5MzZQI

There is some confusing about the version: Zenodo has a 1.1.0 prior to this 1.0.1 -- this is not standard; can you please fix it.

Good catch! This was a mistake on my part.
The previous release on zenodo was supposed to be 0.1.0, but I apparently typed in 1.1.0 instead. I have fixed this mistake. So now the versions should make more sense: https://zenodo.org/record/3386122#.YKZPhZMzZQI
Note that this mistake is only present on zenodo, but neither on CRAN nor on GitHub versions.

Let me know if there is anything else to fix.

@mikldk
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mikldk commented May 20, 2021

@IndrajeetPatil:

Zenodo:
statsExpressions: Tidy Dataframes and Expressions with Statistical Details

JOSS:
statsExpressions: R Package for Tidy Dataframes and1Expressions with Statistical Details

@IndrajeetPatil
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IndrajeetPatil commented May 20, 2021

Oops, sorry, fixed: https://zenodo.org/record/4773886#.YKZT5JMzZQI

@mikldk
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mikldk commented May 20, 2021

@whedon accept

@whedon whedon added the recommend-accept Papers recommended for acceptance in JOSS. label May 20, 2021
@whedon
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whedon commented May 20, 2021

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented May 20, 2021

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

Check final proof 👉 openjournals/joss-papers#2326

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2326, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

@whedon
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whedon commented May 20, 2021

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.03139 is OK
- 10.21105/joss.01412 is OK
- 10.21105/joss.02306 is OK
- 10.31234/osf.io/p7mku is OK
- 10.3758/s13428-019-01246-w is OK
- 10.21105/joss.01541 is OK
- 10.21105/joss.01686 is OK
- 10.3758/s13423-020-01798-5 is OK
- 10.32614/RJ-2016-001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@IndrajeetPatil
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Thanks everyone for your feedback and one of the smoothest and most helpful reviews processes ever! ❤️

@kyleniemeyer
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@whedon accept deposit=true

@whedon
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whedon commented May 20, 2021

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

@whedon whedon added the published Papers published in JOSS label May 20, 2021
@whedon
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whedon commented May 20, 2021

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented May 20, 2021

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03236 joss-papers#2327
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03236
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@kyleniemeyer
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Congrats @IndrajeetPatil on your article's publication in JOSS!

Many thanks to @humanfactors and @tomfaulkenberry for reviewing this, and @mikldk for editing.

@whedon
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whedon commented May 20, 2021

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03236/status.svg)](https://doi.org/10.21105/joss.03236)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03236">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03236/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03236/status.svg
   :target: https://doi.org/10.21105/joss.03236

This is how it will look in your documentation:

DOI

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