[REVIEW]: splithalf: robust estimates of split half reliability

[whedon]

Submitting author: @sdparsons (Sam Parsons)
Repository: https://github.com/sdparsons/splithalf/
Version: v0.8.1
Editor: @oliviaguest
Reviewer: @jpsnijder, @Nathaniel-Haines, @rMassimiliano
Archive: 10.6084/m9.figshare.11956746.v5

⚠️ 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 badge code:

HTML: <a href="https://joss.theoj.org/papers/95702864aacb75b06f30e9e0c842d7b8"><img src="https://joss.theoj.org/papers/95702864aacb75b06f30e9e0c842d7b8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/95702864aacb75b06f30e9e0c842d7b8/status.svg)](https://joss.theoj.org/papers/95702864aacb75b06f30e9e0c842d7b8)

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

@jpsnijder & @Nathaniel-Haines & @rMassimiliano, 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 @oliviaguest 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 @jpsnijder

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 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 (@sdparsons) 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: 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?
• 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: Do the authors clearly state 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 @Nathaniel-Haines

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 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 (@sdparsons) 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: 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?
• 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: Do the authors clearly state 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 @rMassimiliano

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 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 (@sdparsons) 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: 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?
• 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: Do the authors clearly state 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jpsnijder, @Nathaniel-Haines, @rMassimiliano 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.

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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:

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

@whedon generate pdf

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (326.7 files/s, 60692.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                8            354            280           1366
Markdown                         4            203              0            599
TeX                              2             18              0            294
Rmd                              2            176            210            131
C++                              2             11              4             25
YAML                             1              1              4             18
C                                1              4              4             14
-------------------------------------------------------------------------------
SUM:                            20            767            502           2447
-------------------------------------------------------------------------------


Statistical information for the repository '63657c5c53d103363103e795' was
gathered on 2021/02/15.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Sam Parsons                      2            80             10           86.54
sdparsons                        1             3             11           13.46

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
sdparsons                    62         2066.7          0.4               12.90

[whedon]

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

[whedon]

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

OK DOIs

- doi.org/10.1177/2515245919879695 is OK
- 10.12688/wellcomeopenres.15191.1 is OK
- 10.31234/osf.io/y6tcz is OK
- 10.2307/1412159 is OK
- 10.3758/s13428-017-0935-1 is OK

MISSING DOIs

- 10.1201/b15166 may be a valid DOI for title: Dynamic Documents with R and knitr

INVALID DOIs

- None

[oliviaguest]

Hi all! 👋 Thank you so much, @jpsnijder, @Nathaniel-Haines, @rMassimiliano for accepting to review this. Please read the instructions above. If you have trouble ticking things off in the list above, remember you need to click to "accept" here: https://github.com/openjournals/joss-reviews/invitations! Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread, so we can all keep track of them. 🌸

For examples of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

[Nathaniel-Haines]

Hi @oliviaguest, thanks for setting this up! It looks like my invite may have expired, as I cannot check the boxes, and when I follow the acceptance link, I get a message saying that either the invite expired or no longer exists/was revoked.

Are you able to re-invite me?

[oliviaguest]

@whedon re-invite @Nathaniel-Haines as reviewer

[whedon]

OK, the reviewer has been re-invited.

@Nathaniel-Haines please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[jpsnijder]

Dear @oliviaguest,

here are some additional notes and comments on the current review. If items are not listed here, then they were checked off without any issues or warranting a comment.

Overall, the package is in good shape and I can't foresee any issues with widespread use of it.
minor: https://github.com/sdparsons/splithalf states that the current version = 0.7.1; provided code installs 0.7.2
(I don't see why I would open an issue for this @sdparsons)

General checks
All ✅
Functionality
All ✅
Additionally;

• installs fine on current R/Rstudio versions, as well as on an older version (R3.6).
• ran all functions on private data; no issues and run as expected.

Documentation
All ✅
Software paper
All ✅

[whedon]

👋 @jpsnijder, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @Nathaniel-Haines, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @rMassimiliano, please update us on how your review is going (this is an automated reminder).

[oliviaguest]

@jpsnijder thanks for your review so far!

I suggest you submit a PR for the clarification you require — probably it's to this file, if I understand your requirements: https://github.com/openjournals/joss/blob/master/app/views/shared/review_body.text.erb

[jpsnijder]

Hi @oliviaguest, I am not sure how that works exactly. But I have submitted an issue with the journal as well.
Just to clarify: Under the Documentation section of the checklist there is the statement of need item that refers to "the paper" (i.e., A statement of need: Does the paper have a section titled). Does "the paper" here refer to the software paper or the documentation? If it refers to the software paper then it seems like the items are under their wrong respective sections (or; they are swapped). Before I complete the review, I figured I get some clarification on this.

[Nathaniel-Haines]

Hi @sdparsons! I have a few minor notes on the github instructions and the JOSS paper.

1. it looks like the "Installation" header in the markdown file on the main github page is not being rendered properly:

2. I wonder if the instructions for the second step in the multiverse analysis is incomplete? For example, in the image below, the instructions say: "The key difference here is ...", which makes me think that "..." should be replaced by something specific? Image of the part in question here:

3. In the JOSS paper itself, it appears that an in-text citation is missing in the statement of need, where only "(2019)" appears on line 21 without an author attribution:

[Nathaniel-Haines]

Hi @oliviaguest, after passing through everything, I agree with @jpsnijder that things look good overall! I do have a few concerns that I think are worth addressing. The minor ones are those in the comment in this thread directly above this message (here: #3041 (comment)). I have a few other less minor concerns that I submitted as issues:

1. The first is listed here: Plotting error for score = "difference_of_difference" argument sdparsons/splithalf#8, which details an error I get when using the plotting function for one of the main analyses. Note that the results look fine, but the plot is not generated correctly.

2. The second is listed here: Validation of estimates sdparsons/splithalf#9, which is a concern regarding validation/whether the package performs as expected. In the simple example I ran, it does give results consistent with, but not identical to, a different package designed to estimate split-half reliability. That said, I think it would be good for users to see that the main functionality has been validated either with some simple simulations or with more comprehensive comparison against other similar software results. I think this could also help contextualize how the package is different from other common packages in the field, which was not immediately apparent to me from what is described in the documentation until I compared them in more detail.

For these reason, I have left the "Functionality", "Automated tests", and "State of the field" checks unticked for now until we get a chance to discuss in more detail. Note that I have also left the "References" check unticked due to (3) in my aforementioned minor comment.

[rMassimiliano]

Hi @oliviaguest, my invite is expired, could you re-invite me please?

[danielskatz]

@whedon re-invite @rMassimiliano as reviewer

[whedon]

OK, the reviewer has been re-invited.

@rMassimiliano please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[oliviaguest]

@jpsnijder OK, it looks all resolved now — thanks and I hope you can now continue unheeded with your review. ☺️

[jpsnijder]

@jpsnijder OK, it looks all resolved now — thanks and I hope you can now continue unheeded with your review. ☺️

Hi @oliviaguest, is there anything else for me to do when I finished the checklist and posted additional notes in this comment section?

[sdparsons]

@oliviaguest I made some minor changes and added a reference to the paper. All looks ready to go for me :)

[oliviaguest]

Amazing! Fabulous! ☺️

[oliviaguest]

@whedon check repository

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.12 s (174.4 files/s, 41435.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                                8            364            592           1402
Rmd                              3            283            334            804
Markdown                         4            206              0            606
TeX                              2             18              0            295
C++                              2             11              4             25
YAML                             1              1              4             18
C                                1              4              4             14
-------------------------------------------------------------------------------
SUM:                            21            887            938           3164
-------------------------------------------------------------------------------


Statistical information for the repository '4634e50457eb680e0ba2ab60' was
gathered on 2021/04/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Sam Parsons                      2            80             10           86.54
sdparsons                        1             3             11           13.46

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
sdparsons                    62         2066.7          0.4               12.90

[oliviaguest]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2257

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2257, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[oliviaguest]

@sdparsons what is the right version? Is it correct above?

[whedon]

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

OK DOIs

- 10.1201/b15166 is OK
- doi.org/10.1177/2515245919879695 is OK
- 10.12688/wellcomeopenres.15191.1 is OK
- 10.31234/osf.io/y6tcz is OK
- 10.2307/1412159 is OK
- 10.3758/s13428-017-0935-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[oliviaguest]

@whedon set v0.8.1 as version

[whedon]

OK. v0.8.1 is the version.

[oliviaguest]

@whedon generate pdf

[whedon]

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

[sdparsons]

@oliviaguest yeah 0.8.1, and the proof looks good!
Thank you for shepherding this through :)

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2258

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2258, 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]

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

OK DOIs

- 10.1201/b15166 is OK
- doi.org/10.1177/2515245919879695 is OK
- 10.12688/wellcomeopenres.15191.1 is OK
- 10.31234/osf.io/y6tcz is OK
- 10.2307/1412159 is OK
- 10.3758/s13428-017-0935-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03041 joss-papers#2259
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03041
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...

[arfon]

@jpsnijder, @Nathaniel-Haines, @rMassimiliano - many thanks for your reviews here and to @oliviaguest for editing this submission! JOSS relies upon the volunteer efforts of people like you, and we simply wouldn't be able to do this without you ✨

@sdparsons - your paper is now accepted and published in JOSS ⚡🚀💥

[whedon]

🎉🎉🎉 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.03041/status.svg)](https://doi.org/10.21105/joss.03041)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03041">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03041/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03041/status.svg
   :target: https://doi.org/10.21105/joss.03041

This is how it will look in your documentation:

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[sdparsons]

This is very exciting, thank you all!
A huge thank you to @jpsnijder, @Nathaniel-Haines, @rMassimiliano. Your input pushed me to fix a bunch of issues I would not have spotted if it were not for your input and massively improve the documentation around splithalf. This has by far felt like the most productive review process I have been part of. Thank you @oliviaguest too for editing and guiding all of us through this great process. I really appreciate all of your time and expertise. I've added my name to the reviewer list, so hopefully I'll be on the other side of this process soon to give back :)

[oliviaguest]

@sdparsons amazing — I'm so glad to hear this! ☺️