[REVIEW]: R for marine ecologists: wrangling Earth System Model outputs

[editorialbot]

Submitting author: @JessicaBolin (Jessica Bolin)
Repository: https://github.com/JessicaBolin/esmRworkshop_notes
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @bleds22e
Reviewers: @mjanuario, @rachtorr
Archive: Pending
Paper kind: learning module

Status

Status badge code:

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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

@mjanuario & @rachtorr, 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://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html. Any questions/concerns please let @bleds22e 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 @rachtorr

📝 Checklist for @mjanuario

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

✅ OK DOIs

- 10.1002/lob.10113 is OK
- 10.21105/jose.00037 is OK
- 10.1002/ecs2.2567 is OK
- 10.1016/j.tree.2023.04.005 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Incorporating climate data into the decision makin...
- No DOI given, and none found for title: Improving code reproducibility: Small steps with b...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Repository Analysis Report

Code breakdown

github.com/AlDanial/cloc v 1.98  T=0.14 s (629.5 files/s, 359560.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            46           1437            184          36617
Bourne Shell                     6            960            744           4544
CSS                              5             39             30           2239
JavaScript                      11            235            226           2112
JSON                             2              0              0            974
R                               14            324            266            636
TeX                              2             33              0            186
Markdown                         2             26              0             89
YAML                             3              8              4             63
-------------------------------------------------------------------------------
SUM:                            91           3062           1454          47460
-------------------------------------------------------------------------------

Commit Count by Author

35	Jessica A. Bolin

Repository History

Repository age: First commit on January 07, 2025

Code distribution (top 3 48-hour windows):

Period	Insertions	% of Total	Signal	View Changes
May 27, 2025 - May 29, 2025	20740	61.5%	🟠	View diff
Jan 05, 2025 - Jan 07, 2025	5424	16.1%	🟢	View commit
Aug 03, 2025 - Aug 05, 2025	4143	12.3%	🟢	View diff

GitHub Activity Metrics

Metric	Count
GitHub stars	1
Forks	0
GitHub contributors	1
Releases	0
Total issues	0
Total pull requests	0
Unique commenters/reviewers (excluding authors)	0

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1187

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[rachtorr]

Review checklist for @rachtorr

Conflict of interest

• 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

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

General checks

• Repository: Is the source for this learning module available at the https://github.com/JessicaBolin/esmRworkshop_notes?
• 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)
• Version: Does the release version given match the repository release?
• Authorship: Has the submitting author (@JessicaBolin) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• 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!)

• 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.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• 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

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

Update 7/6/2026: full comments can be found on the issue page here: JessicaBolin/esmRworkshop_notes#1
Great job on this! @JessicaBolin

[mjanuario]

Review checklist for @mjanuario

Conflict of interest

• 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

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

General checks

• Repository: Is the source for this learning module available at the https://github.com/JessicaBolin/esmRworkshop_notes?
• 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)
• Version: Does the release version given match the repository release?
• Authorship: Has the submitting author (@JessicaBolin) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

• A statement of need: Do the authors clearly state the need for this module and who the target audience is?
• Installation instructions: Is there a clearly stated list of dependencies?
• Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
• 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!)

• 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.)
• Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
• Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
• Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
• 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

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

[mjanuario]

Hi @JessicaBolin ,

Nice work on the workshop materials. I've completed my review for now, and any unchecked items on my checklist indicate a need for additional work. Feel free to refer to my own repo for examples of how I addressed software release, archiving, and other publication requirements: https://github.com/mjanuario/evolved

To summarize the main points:

• Create a formal release of the workshop. The repository should include a GitHub release (e.g., using the Releases feature): https://github.com/JessicaBolin/esmRworkshop_notes/releases
• Archive the workshop in a permanent repository. JOSE’s policy is not 100% clear if this is a must, but here is github’s instruction on how to do it as linked in JOSE site: https://guides.github.com/activities/citable-code/ . I archived mine using Zenodo, which is free to the point I remember.
• State the target audience in the "Statement of Need" section. This would help communicate more clearly who the workshop is intended for. A short sentence is enough for me.
• Reference issues I've found and should flag for the editor:
* I could not find the reference for Halpin et al. (2014).
* Kellie, D., & Westgate appears to be a website post rather than a formal publication. I'm not sure whether JOSE accepts this type of source as a reference, so I will flag it for the editor to consider.