[REVIEW]: EdSurvey: an R package to analyze Large-scale educational assessments data

[editorialbot]

Submitting author: @pdbailey0 (Paul Bailey)
Repository: https://github.com/American-Institutes-for-Research/EdSurvey/
Branch with paper.md (empty if default branch): joss
Version: 4.0.1
Editor: @oliviaguest
Reviewers: @wjakethompson, @jrosen48
Archive: Pending

Status

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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

@wjakethompson & @jrosen48, 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 @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 ✨

Checklists

📝 Checklist for @wjakethompson

[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:

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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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.54 s (621.1 files/s, 147904.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                              215           5042           8657          35345
HTML                           102           4135            311          14426
JavaScript                       4           2099           1928           7019
XML                              1              0              0            306
Markdown                         4             57              0            176
TeX                              1              7              0             67
YAML                             3              3              4             27
SVG                              1              0              1             11
Rmd                              2             63             81              9
CSS                              1              0              5              1
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           335          11406          10987          57388
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1081

[editorialbot]

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

OK DOIs

- 10.18637/jss.v081.i07 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[oliviaguest]

👋 Hi @wjakethompson, @jrosen48, thank you so much for helping out at JOSS. If you need any pointers, please feel free to look at previous reviews (which can be found by looking at published papers) and the documentation. If you need to comment on the code itself, opening an issue at the repo and then linking to it from here (to help me/others keep track) is the way to go. For comments on the paper, you can also open issues or PRs (say for typos), but those can be directly posted as replies in this issue. Thanks, and feel free to reach out if you need me. ☺️

[wjakethompson]

Review checklist for @wjakethompson

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/American-Institutes-for-Research/EdSurvey/?
• 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 (@pdbailey0) 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?

[wjakethompson]

I have completed my review, with a few outstanding issues:

1. Currently there is no LICENSE file. I have opened a PR to add this document. crossref: Add license file American-Institutes-for-Research/EdSurvey#61
2. There are currently no contributor guidelines, just a mention in the README that contributions will be considered. Specific guidelines should be added, and I would also recommend adding a code of conduct. crossref: Add community guidelines American-Institutes-for-Research/EdSurvey#63
3. Test coverage is very low (~15%) and does not appear to be automated. I think this should be substantially higher to meet the documentation criterion. crossref: Automate and increase test coverage American-Institutes-for-Research/EdSurvey#62
4. A few recommendations from goodpractice::gp() to ensure functionality of the package works as intended. crossref: Code functionality issues American-Institutes-for-Research/EdSurvey#64
5. Example uses are pre-rendered and often several years old, making it unclear whether these examples are still relevant, or will remain relevant. crossref: Example usage questions American-Institutes-for-Research/EdSurvey#65

[oliviaguest]

@wjakethompson thank you so much. @pdebuyl is it clear what needs to be done for the next steps? 😊

[pdbailey0]

@oliviaguest I think you intended to at tag me, so I'll respond. Yes, it is clear what I should do, I'm working on my response. EdSurvey is a pretty large and mature package. As an example, I have over a hundred sapplys to look at!

[oliviaguest]

@oliviaguest I think you intended to at tag me, so I'll respond. Yes, it is clear what I should do, I'm working on my response. EdSurvey is a pretty large and mature package. As an example, I have over a hundred sapplys to look at!

Indeed, that autocomplete with a migraine is not ideal. 😂

[oliviaguest]

@editorialbot generate pdf

[editorialbot]

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

[jrosen48]

So sorry to drop the ball on this. Is my review, keeping in mind @wjakethompson's comments, still helpful/needed?

[pdbailey0]

@jrosen48 your question is probably best addressed by @oliviaguest, but I will say that I just started working on wrapping up @wjakethompson thoughtful comments last week so I'd still appreciate it.

[oliviaguest]

@jrosen48 please do review this! Thank you! 😊 2 reviewers are always better, if not required in most cases, and we'd appreciate your feedback.

[oliviaguest]

@jrosen48 do you have an ETA for us? ☺️

[jrosen48]

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

General Checks

• Repository: Is the source code for this software available at the https://github.com/American-Institutes-for-Research/EdSurvey/?
• 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 (@pdbailey0) 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?

[jrosen48]

I've also completed my review. A few additional notes:

1. I filed an issue here: https://github.com/American-Institutes-for-Research/EdSurvey/issues
2. I am having a bit of a hard time understanding the nature and extent of the automated tests (in part because there seem to be many - a good issue)! Is it possible to separate the files with the tests from the data/output used as part of them (here)? Alternatively, could the testing coverage be automatically displayed via https://covr.r-lib.org? EDIT - I now see Automate and increase test coverage American-Institutes-for-Research/EdSurvey#62, I am not quite sure what to recommend here - at the cost-benefit margin, is it possible to enhance the test coverage above its present value (around 15%)?
3. While the paper is well-written and the diagram for the workflow is important and valuable, could the paper include a minimal example of the code used to access and conduct a minimal analysis using the package?

[oliviaguest]

@pdbailey0 are you taking a look at the above/making any edits?

[pdbailey0]

Yes, sorry, I've been talking this over with my team and deciding what the best response to the vignette one is.

[yuqiliao]

Hi @jrosen48 , thanks for your review and feedback!

We're actively addressing your first two points. Regarding note 3 about including a minimal code example, we've followed the submission guidelines closely. As per the guidelines, a “full length” paper is not permitted, and software documentation such as API (Application Programming Interface) functionality should not be in the paper and instead should be outlined in the software documentation.

Therefore, in our manuscript, we refrained from including code snippets but ensured comprehensive examples are included in our documentation. These examples are accessible via function calls using ? and are also available in our online user's guide here. Would resolving note 3 without any changes be acceptable to you?

[jrosen48]

Appreciate the response and the reasoning. Isn't a minimal example different from documentation of an API, though? Just looking for one example of one API call - not API documentation.

[pdbailey0]

I think we're interpreting the guidelines as as not allowing it. But if @oliviaguest says it is allowable, we're happy to include it.