Joss-reviews: [REVIEW]: effectsize: Estimation and Interpretation of Effect Size Indices and Standardized Parameters

[whedon]

Submitting author: @mattansb (Mattan S. Ben-Shachar)
Repository: https://github.com/easystats/effectsize
Version: 0.4.0.001
Editor: @mikldk
Reviewer: @trashbirdecology, @jkarreth
Archive: Pending

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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

@trashbirdecology & @jkarreth, 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 @trashbirdecology

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 repository url?
• [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 (@mattansb) 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?
• [ ] 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [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?

Review checklist for @jkarreth

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 repository url?
• [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 (@mattansb) 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?
• [ ] 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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [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?

[whedon]

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

:warning: JOSS reduced service mode :warning:

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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To fix this do the following two things:

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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]

PDF failed to compile for issue #2815 with the following error:

Can't find any papers to compile :-(

[mikldk]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #2815 with the following error:

Can't find any papers to compile :-(

[arfon]

Can't find any papers to compile :-(

Lemme dig into this @mikldk - not sure what is going on here.

[mikldk]

@mattansb (and possibly @arfon): When I look into the repo, it is not clear if the software submitted is at the master branch or in the paper branch?

[mikldk]

@trashbirdecology, @jkarreth: Thanks for agreeing to review. We are having some small technical issues. We will let you know when you can start the review. Please wait until we say "go".

(@mattansb, @jkarreth: Note that we have a slightly extended time frame at the moment, and @jkarreth do not expect to be able to complete their review before mid-December, but will try if at all possible.)

[arfon]

@whedon generate pdf from branch paper

[whedon]

Attempting PDF compilation from custom branch paper. Reticulating splines etc...

[whedon]

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

[arfon]

@mattansb (and possibly @arfon): When I look into the repo, it is not clear if the software submitted is at the master branch or in the paper branch?

I think we're good now ☝️. I accidentally introduced a regression into Whedon last night.

[mikldk]

Thanks, @arfon .

@mattansb: In the paper branch there is a copy of the R package itself and not just the paper for JOSS. @arfon, shouldn't this copy of the R package in the paper branch be removed such that only the paper etc. are in the paper branch?

[arfon]

@mattansb: In the paper branch there is a copy of the R package itself and not just the paper for JOSS. @arfon, shouldn't this copy of the R package in the paper branch be removed such that only the paper etc. are in the paper branch?

We generally don't insist on this but it would be good to clarify for the reviewers here which branch of the _software_ should be reviewed.

[mattansb]

@arfon & @mikldk The paper branch has a copy of the current CRAN version of the package. But I think it will reduce ambiguity if I just merge the paper branch into master, so I'll do that now. Sorry about the confusion.

[mattansb]

Done.

Again, sorry for any mix up.

[mikldk]

@mattansb: No worries -- I just wanted to be sure that reviewers looked at the right branch. So to be sure (the paper branch still has the code?): The reviewers should look at the code in the master branch and the paper in the paper branch?

[mattansb]

@mikldk Reviewers should look at the master branch which now has both the code and the paper.

[mikldk]

@mikldk Reviewers should look at the master branch which now has both the code _and_ the paper.

Thanks, @mattansb . You should consider deleting the paper branch.

[mikldk]

@whedon generate pdf

[whedon]

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

[mikldk]

@trashbirdecology, @jkarreth: Once again, thanks for agreeing to review. The problems are now resolved, and the master branch is ready for your reviews. 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.

(@mattansb, @jkarreth: Note that we have a slightly extended time frame at the moment, and @jkarreth do not expect to be able to complete their review before mid-December, but will try if at all possible.)

[trashbirdecology]

Review issue opened at repository.

[whedon]

:wave: @trashbirdecology, please update us on how your review is going.

[whedon]

:wave: @jkarreth, please update us on how your review is going.

[trashbirdecology]

Checked off everything except functionality as I still need to go through each function. Will try to do that by Monday, @mattansb

[mattansb]

@whedon generate pdf

[whedon]

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

[trashbirdecology]

@mattansb just noticed --"Sums" or "Sum" of Squares?

[mattansb]

Usually "sum of squares", but the context here is of several of these (these functions in MOTE and MBESS require more than one sum of squares for the computation of each effect size).