[REVIEW]: An R reproducibility toolkit for the practical researcher

[editorialbot]

Submitting author: !--author-handle-->@paocorrales<!--end-author-handle-- (Paola Corrales) Repository: https://github.com/eliocamp/reproducibility-with-r/ Branch with paper.md (empty if default branch): Version: v1.2.0 Editor: !--editor-->@yabellini<!--end-editor-- Reviewers: @Aariq, @luisDVA Archive: Pending Paper kind: learning module

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Reviewers and authors:

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Reviewer instructions & questions

@Aariq, 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:

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✨ 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 @Aariq

📝 Checklist for @luisDVA

[editorialbot]

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[editorialbot]

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

✅ OK DOIs

- 10.1016/j.cogpsych.2010.05.004 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: The Turing Way: Sharing the Responsibility of Repr...
- No DOI given, and none found for title: Spaced Practice

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.84 s (557.7 files/s, 165788.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              2              1              0          53770
HTML                           152          14984            166          22910
SVG                              7              1              3          19636
Sass                            98           1793            244          11009
Markdown                        78           1551              0           4131
JavaScript                      57            942            982           3426
XML                             26            156              0           1200
CSS                             21            139             76            789
TeX                              4             42             30            371
TOML                             4             33             64            305
R                                5             24            142             49
JSON                             5              0              0             45
YAML                             5              0              1             23
Rmd                              5            111            277              6
-------------------------------------------------------------------------------
SUM:                           469          19777           1985         117670
-------------------------------------------------------------------------------

Commit count by author:

   145  Elio Campitelli
    42  Pao
    28  Pao Corrales

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1073

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 License found: Creative Commons Attribution 4.0 International (Not OSI approved)

[editorialbot]

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

[Aariq]

Review checklist for @Aariq

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• [x] Repository: Is the source for this learning module available at the https://github.com/eliocamp/reproducibility-with-r/?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• [x] Version: Does the release version given match the repository release?
• [x] Authorship: Has the submitting author (@paocorrales) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• [x] Installation instructions: Is there a clearly stated list of dependencies?
• [x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• [x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• [x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• [x] Description: Does the paper describe the learning materials and sequence?
• [x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• [x] Could someone else teach with this module, given the right expertise?
• [x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
  • The Turing Way is referenced with a link to a zenodo record rather than the DOI for that record. Might be better to use https://doi.org/10.5281/zenodo.2669548

These are great materials and the short paper introduces them well. I teach a workshop series that covers similar topics and I'm very excited to adopt some of the materials. I think the guide is written very thoughtfully with their target audience in mind. I especially appreciated the discussion of what reproducibility is and how it is not necessarily related to correctness and isn't a binary. As I was going through the materials on reproducibility.rocks, I opened a few minor issues:

• https://github.com/eliocamp/reproducibility-with-r/issues/24
• https://github.com/eliocamp/reproducibility-with-r/issues/25
• https://github.com/eliocamp/reproducibility-with-r/issues/26
• https://github.com/eliocamp/reproducibility-with-r/issues/28

These issues mostly relate to content that is slightly out of date. I'll also note that while it is true that Quarto is still rapidly evolving, I think very soon (if not already) it will be worth it to teach Quarto instead of RMarkdown for reproducible scientific manuscripts and reports. RMarkdown and the rticles package certainly aren't going away anytime soon, but some of the frustrations I've encountered writing manuscripts in RMarkdown have been solved in Quarto—e.g. cross references to equations, images, code chunks, and other arbitrary sections—and I don't think Posit plans to actively develop RMarkdown going forwards. The authors may want to consider prioritizing an update to the reproducible reporting section in the next revision of these materials, although I do not think this update is necessary for acceptance of the manuscript.

[eliocamp]

Thanks for the review and the open issues. I've fixed 3/4. The missing one seems to be a limitation of the theme we're using for the website. I've open an issue in that repository to see what we can do.

And yes on quarto. We hadn't looked at the list of available journal templates for a while, so we didn't know it was so large (although not as large as rticles). We would need to look how to use a custom LaTeX template with quarto.

[yabellini]

@Aariq thank you so much for your review.

[yabellini]

@editorialbot add @luisDVA as reviewer

[editorialbot]

@luisDVA added to the reviewers list!

[yabellini]

Hello @luisDVA, thank you so much for agreeing to review this proposal 🙏 .

I added you as a reviewer. You can generate your checklist by calling our bot:

@ editorialbot generate my checklist

[paocorrales]

Hello! We'll be teaching the workshop this week and are making the usual checks and updates to the material. We haven't changed anything big, just broken links and small additions. I wanted to mention it here in case anyone is currently visiting the web or the repo!

[luisDVA]

Review checklist for @luisDVA

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSE conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSE code of conduct.

General checks

• [x] Repository: Is the source for this learning module available at the https://github.com/eliocamp/reproducibility-with-r/?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
• [x] Version: Does the release version given match the repository release?
• [x] Authorship: Has the submitting author (@paocorrales) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• [x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• [x] Installation instructions: Is there a clearly stated list of dependencies?
• [x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• [x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

• [x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
• [x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• [x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• [x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• [x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
• [x] Description: Does the paper describe the learning materials and sequence?
• [x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
• [x] Could someone else teach with this module, given the right expertise?
• [x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
• [x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?