[REVIEW]: Can you predict the future? A tutorial for the National Ecological Observatory Network Ecological Forecasting Challenge #259

editorialbot · 2024-09-16T08:36:36Z

Submitting author: @OlssonF (Freya Olsson)
Repository: https://github.com/eco4cast/NEON-forecast-challenge-workshop
Branch with paper.md (empty if default branch): main
Version: v1.3.1
Editor: @acocac
Reviewers: @dlebauer, @skmorgane
Archive: 10.5281/zenodo.14018090
Paper kind: learning module

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/37e9e48c49abf89a619b787d106d79bd"><img src="https://jose.theoj.org/papers/37e9e48c49abf89a619b787d106d79bd/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/37e9e48c49abf89a619b787d106d79bd/status.svg)](https://jose.theoj.org/papers/37e9e48c49abf89a619b787d106d79bd)

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

@dlebauer & @acocac, 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 @acocac 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 @dlebauer

📝 Checklist for @skmorgane

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-09-16T08:36:38Z

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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editorialbot · 2024-09-16T08:36:54Z

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

✅ OK DOIs

- 10.5281/zenodo.8316965 is OK
- 10.1002/fee.2616 is OK
- 10.1002/ecs2.2567 is OK
- 10.21105/joss.01686 is OK
- 10.1073/pnas.1710231115 is OK
- 10.1111/2041-210X.13955 is OK
- 10.1515/9781400885459 is OK
- 10.21105/jose.00198 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-09-16T08:37:22Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (755.2 files/s, 241591.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         5            464              0           1822
Rmd                              3            366            648            511
R                                3             53             44            114
TeX                              1              9              0            105
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            13            893            696           2570
-------------------------------------------------------------------------------

Commit count by author:

   151	LAPTOP-FO87M896reya
    28	Freya Olsson
     4	rqthomas
     3	github-actions
     2	Cayelan Carey
     1	Carl Boettiger
     1	Mary Lofton
     1	Quinn Thomas
     1	QuinnThomas

editorialbot · 2024-09-16T08:37:26Z

Paper file info:

📄 Wordcount for paper.md is 1662

✅ The paper includes a Statement of need section

editorialbot · 2024-09-16T08:37:28Z

License info:

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

editorialbot · 2024-09-16T08:37:31Z

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

acocac · 2024-09-23T06:43:27Z

@editorialbot add @skmorgane as reviewer

editorialbot · 2024-09-23T06:43:30Z

@skmorgane added to the reviewers list!

acocac · 2024-09-23T06:45:39Z

@editorialbot remove @acocac as reviewer

editorialbot · 2024-09-23T06:45:41Z

@acocac removed from the reviewers list!

acocac · 2024-09-23T06:49:48Z

Hi @OlssonF
fyi - I got a late reply from one of your suggested reviewers, Morgan Ernest, who has confirmed availability within a time period of 3 weeks. I hope this is fine for you. I'll remove myself from the reviewer list.

acocac · 2024-09-23T06:50:42Z

👋 @dlebauer @skmorgane we will conduct the review in this issue.

Please read through the above information and let me know if you have any questions about the review process.

Thank you 🙏

dlebauer · 2024-09-30T22:03:21Z

Review checklist for @dlebauer

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/OlssonF/NEON-forecast-challenge-workshop?
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 (@OlssonF) 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)?

dlebauer · 2024-09-30T22:15:59Z

@acocac Could you please help me understand the version requirement "Does the release version given match the repository release?" - the latest release in the repository is v1.2.0, this issue lists it as v1.1.0. It isn't clear to me which version the proof is from, though I suspect any changes will at least bump the version.

--> I think it would be helpful to clarify this part of the checklist and reviewer instructions

acocac · 2024-10-01T11:01:37Z

@editorialbot commands

editorialbot · 2024-10-01T11:01:40Z

Hello @acocac, here are the things you can ask me to do:


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# Adds a checklist for the reviewer using this command
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@editorialbot set v1.0.0 as version

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@editorialbot set jose-paper as branch

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@editorialbot set https://github.com/organization/repo as repository

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@editorialbot set 10.5281/zenodo.6861996 as archive

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@editorialbot create post-review checklist

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acocac · 2024-10-01T11:02:16Z

@editorialbot set v1.2.0 as version

editorialbot · 2024-10-01T11:02:19Z

Done! version is now v1.2.0

acocac · 2024-10-01T11:03:14Z

@acocac Could you please help me understand the version requirement "Does the release version given match the repository release?" - the latest release in the repository is v1.2.0, this issue lists it as v1.1.0. It isn't clear to me which version the proof is from, though I suspect any changes will at least bump the version.

--> I think it would be helpful to clarify this part of the checklist and reviewer instructions

@dlebauer - I've fixed the issue. The revision should be on the latest release.

skmorgane · 2024-10-04T14:32:55Z

Review checklist for @skmorgane

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/OlssonF/NEON-forecast-challenge-workshop?
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 (@OlssonF) 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)?

skmorgane · 2024-10-04T14:46:16Z

@acocac I started my review by making sure I didn't have conflicts with the full author list but realized that two of the authors I have an association with that I should disclose: Carey and Thomas. We are coauthors on a large author line paper that was just accepted. I think this one falls under "co-authors but not really collaborating" in the guidelines and is probably not a concern. However, we are also collaborating on a proposal, again a large multi-investigator/multi-institutional effort, but we do interact a little more directly there. I think I can review this impartially, but if the association violates JOSE rules, I have two people I can recommend as reviewers who I know are not interacting with anyone on the author line. Just let me know how you would like to proceed

While reviewing for openjournals/jose-reviews#259 I found a few changes to suggest: I added a few hyperlinks to local files - however it is done, I think that when files are referenced it should be clear to the reader where to find them - even if they are in the root directory, but especially if not. Should Rstudio be listed as a requirement? The first to methods under getting the code assume it is installed. This also fixes a few typos

OlssonF · 2024-10-22T13:08:56Z

@OlssonF thanks for confirm the successful transfer of the repository. May I ask if you update the paper too? It still points to the previous GitHub repository, https://github.com/OlssonF/NEON-forecast-challenge-workshop. Please commit/push the updated paper and release a version accordingly. Thank you 🙏

Thanks! We have updated the paper and release (https://github.com/eco4cast/NEON-forecast-challenge-workshop/releases/tag/v1.3.1)

acocac · 2024-10-23T09:00:48Z

@editorialbot set v1.3.1 as version

editorialbot · 2024-10-23T09:00:52Z

Done! version is now v1.3.1

acocac · 2024-10-30T10:54:58Z

acocac · 2024-10-30T10:56:22Z

@OlssonF prior to acceptance of the submission, I kindly ask your help to complete the additional author tasks i.e. checklist above.

OlssonF · 2024-10-31T13:47:29Z

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSE paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSE paper.
Make sure that the license listed for the archive is the same as the software license.

The latest software release is v1.3.1 (https://github.com/eco4cast/NEON-forecast-challenge-workshop/releases/tag/v1.3.1) and the Zenodo DOI is https://doi.org/10.5281/zenodo.14018090. I have checked and updated the Zenodo archive title and authorship and updated the license to match the GitHub repository (MIT license)
Thanks @acocac

acocac · 2024-11-01T11:50:13Z

@editorialbot check references

editorialbot · 2024-11-01T11:50:33Z

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

✅ OK DOIs

- 10.5281/zenodo.8316965 is OK
- 10.1002/fee.2616 is OK
- 10.1002/ecs2.2567 is OK
- 10.21105/joss.01686 is OK
- 10.1073/pnas.1710231115 is OK
- 10.1111/2041-210X.13955 is OK
- 10.1515/9781400885459 is OK
- 10.21105/jose.00198 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

acocac · 2024-11-01T11:51:58Z

@editorialbot generate pdf

editorialbot · 2024-11-01T11:54:02Z

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

acocac · 2024-11-01T11:56:58Z

@editorialbot set https://doi.org/10.5281/zenodo.14018090 as archive

editorialbot · 2024-11-01T11:57:00Z

Done! archive is now 10.5281/zenodo.14018090

acocac · 2024-11-01T11:58:03Z

@editorialbot recommend-accept

editorialbot · 2024-11-01T11:58:05Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-11-01T11:58:18Z

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

✅ OK DOIs

- 10.5281/zenodo.8316965 is OK
- 10.1002/fee.2616 is OK
- 10.1002/ecs2.2567 is OK
- 10.21105/joss.01686 is OK
- 10.1073/pnas.1710231115 is OK
- 10.1111/2041-210X.13955 is OK
- 10.1515/9781400885459 is OK
- 10.21105/jose.00198 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-11-01T11:59:28Z

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/jose-papers#159, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

OlssonF · 2024-11-04T13:59:21Z

Looks good to me @acocac is there anything I need to do?

acocac · 2024-11-14T08:30:39Z

@labarba waiting the final approval. Everything looks ok according to the post-review checklist.

labarba · 2024-11-14T11:57:24Z

patience requested. traveling

labarba · 2024-12-26T19:24:52Z

@editorialbot accept

editorialbot · 2024-12-26T19:24:54Z

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

editorialbot · 2024-12-26T19:26:12Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Olsson
  given-names: Freya
  orcid: "https://orcid.org/0000-0002-0483-4489"
- family-names: Boettiger
  given-names: Carl
  orcid: "https://orcid.org/0000-0002-1642-628X"
- family-names: Carey
  given-names: Cayelan C.
  orcid: "https://orcid.org/0000-0001-8835-4476"
- family-names: Lofton
  given-names: Mary E.
  orcid: "https://orcid.org/0000-0003-3270-1330"
- family-names: Thomas
  given-names: R. Quinn
  orcid: "https://orcid.org/0000-0003-1282-7825"
doi: 10.5281/zenodo.14018090
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Olsson
    given-names: Freya
    orcid: "https://orcid.org/0000-0002-0483-4489"
  - family-names: Boettiger
    given-names: Carl
    orcid: "https://orcid.org/0000-0002-1642-628X"
  - family-names: Carey
    given-names: Cayelan C.
    orcid: "https://orcid.org/0000-0001-8835-4476"
  - family-names: Lofton
    given-names: Mary E.
    orcid: "https://orcid.org/0000-0003-3270-1330"
  - family-names: Thomas
    given-names: R. Quinn
    orcid: "https://orcid.org/0000-0003-1282-7825"
  date-published: 2024-12-26
  doi: 10.21105/jose.00259
  issn: 2577-3569
  issue: 82
  journal: Journal of Open Source Education
  publisher:
    name: Open Journals
  start: 259
  title: Can you predict the future? A tutorial for the National
    Ecological Observatory Network Ecological Forecasting Challenge
  type: article
  url: "https://jose.theoj.org/papers/10.21105/jose.00259"
  volume: 7
title: Can you predict the future? A tutorial for the National
  Ecological Observatory Network Ecological Forecasting Challenge

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-12-26T19:26:16Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2024-12-26T19:26:17Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSE! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.jose.00259 jose-papers#167
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00259
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

labarba · 2024-12-26T19:30:28Z

Congratulations @OlssonF – your JOSE paper is published! 🚀

Huge thanks to our Editor: @acocac and Reviewers: @dlebauer, @skmorgane – your contributions make this possible 🙏

editorialbot · 2024-12-26T19:30:29Z

🎉🎉🎉 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://jose.theoj.org/papers/10.21105/jose.00259/status.svg)](https://doi.org/10.21105/jose.00259)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00259">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00259/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00259/status.svg
   :target: https://doi.org/10.21105/jose.00259

This is how it will look in your documentation:

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editorialbot added R review TeX labels Sep 16, 2024

editorialbot assigned acocac Sep 16, 2024

editorialbot mentioned this issue Sep 16, 2024

[PRE REVIEW]: Can you predict the future? A tutorial for the National Ecological Observatory Network Ecological Forecasting Challenge #232

Closed

editorialbot unassigned acocac Sep 23, 2024

This was referenced Oct 7, 2024

Update README.md eco4cast/NEON-forecast-challenge-workshop#11

Merged

Which documentation? eco4cast/NEON-forecast-challenge-workshop#12

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSE. label Nov 1, 2024

editorialbot added accepted published Papers published in JOSE labels Dec 26, 2024

labarba closed this as completed Dec 26, 2024

[REVIEW]: Can you predict the future? A tutorial for the National Ecological Observatory Network Ecological Forecasting Challenge #259

[REVIEW]: Can you predict the future? A tutorial for the National Ecological Observatory Network Ecological Forecasting Challenge #259

Comments

editorialbot commented Sep 16, 2024 • edited Loading

Status

Reviewer instructions & questions

Checklists

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dlebauer commented Sep 30, 2024 • edited Loading

Review checklist for @dlebauer

Conflict of interest

Code of Conduct

General checks

Documentation

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

JOSE paper

dlebauer commented Sep 30, 2024

acocac commented Oct 1, 2024

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acocac commented Oct 1, 2024

skmorgane commented Oct 4, 2024 • edited Loading

Review checklist for @skmorgane

Conflict of interest

Code of Conduct

General checks

Documentation

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

JOSE paper

skmorgane commented Oct 4, 2024

OlssonF commented Oct 22, 2024

acocac commented Oct 23, 2024

editorialbot commented Oct 23, 2024

acocac commented Oct 30, 2024 • edited by labarba Loading

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

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OlssonF commented Nov 4, 2024 •

edited

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