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[REVIEW]: fishStan: Hierarchical Bayesian models for fisheries #3444

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whedon opened this issue Jul 2, 2021 · 82 comments
Closed
40 tasks done

[REVIEW]: fishStan: Hierarchical Bayesian models for fisheries #3444

whedon opened this issue Jul 2, 2021 · 82 comments
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@marcosvital @BrandonEdwards @Cole-Monnahan-NOAA @MikeKaller
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accepted C++ published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review Stan

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@whedon
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whedon commented Jul 2, 2021 •
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Submitting author: @rerickson-usgs (Richard Erickson)
Repository: https://code.usgs.gov/umesc/quant-ecology/fishstan/
Branch with paper.md (empty if default branch):
Version: v2.0.0
Editor: @marcosvital
Reviewers: @MikeKaller, @Cole-Monnahan-NOAA
Archive: 10.5066/P9TT3ILO

⚠️ JOSS reduced service mode ⚠️

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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196"><img src="https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196/status.svg)](https://joss.theoj.org/papers/34bd0a9673510f204ee01fe1536b2196)

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

@BrandonEdwards & @MikeKaller, 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 @marcosvital 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 @MikeKaller

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@rerickson-usgs) 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

Functionality

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). #3567
  • 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

Review checklist for @Cole-Monnahan-NOAA

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@rerickson-usgs) 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

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)? #3995
  • 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 and who the target audience is?
  • 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?
@whedon whedon mentioned this issue Jul 2, 2021
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@whedon
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whedon commented Jul 2, 2021

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

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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whedon commented Jul 2, 2021 

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (662.5 files/s, 54412.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               44            282           1057           1637
Rmd                              6            217            766            380
Markdown                         6             86              0            343
TeX                              1              6              0             54
JSON                             1              7              0             41
YAML                             1             10              0             41
C/C++ Header                     1              0              1              0
-------------------------------------------------------------------------------
SUM:                            60            608           1824           2496
-------------------------------------------------------------------------------


Statistical information for the repository '39c69dfe28f0b28ed89bba83' was
gathered on 2021/07/02.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Richard A Erickson               2            39             38          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Richard A Erickson            1            2.6          0.0              100.00

@whedon
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whedon commented Jul 2, 2021 

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

OK DOIs

- 10.1002/nafm.10515 is OK

MISSING DOIs

- 10.1016/j.fishres.2015.03.009 may be a valid DOI for title: Spatial and temporal variability in growth of Southern Flounder (Paralichthys lethostigma)
- 10.1201/9781315371986 may be a valid DOI for title: Introductory fisheries analyses with R

INVALID DOIs

- None

@whedon
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whedon commented Jul 2, 2021

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

@marcosvital
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Dear @rerickson-usgs: your manuscript will be reviewed in this issue, and you can reply any comments and suggestions that the reviewers might address right here.

@marcosvital
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@BrandonEdwards and @MikeKaller: thank you again for for accepting review this submission for JOSS.

Even if you are not starting the review right now, please accept the invite, as it has an expiration date (there is a link under Reviewer instructions & questions and you should also get an email notification). Furthermore, please check the instructions and checklists above, and let me know if you need any assistance.

You can also tag @rerickson-usgs if you need to ask specific questions about the submission or to address any changes that might be necessary in the submitted paper or in the repository.

Finally, please let me know if you need any assistance while reviewing.

@whedon
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whedon commented Jul 16, 2021

👋 @MikeKaller, please update us on how your review is going (this is an automated reminder).

@whedon
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whedon commented Jul 16, 2021

👋 @BrandonEdwards , please update us on how your review is going (this is an automated reminder).

@raerickson
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@marcosvital Hope all is well with you. Any updates?

@marcosvital
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Hi, @rerickson-usgs, I was about to ask the reviewers for an update. So here we go:

@BrandonEdwards and @MikeKaller, any news on this review? Let me know if you need any assistance.
And if you haven't started yet, I might need to send a new invitation to allow you to check on the boxes as you move on.

@marcosvital
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Hello again, @rerickson-usgs! It seems that @MikeKaller is generally satisfied with the submission, but there are three issues linked on his reviewing checklist (check above). Did you had the chance to look into them? When addressing them, please create a copy on the original repository if @MikeKaller alredy didn't do that.

@marcosvital
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Dear @BrandonEdwards, did you had the chance to start reviewing this submission? Let me know if you need any assistance, ok?

@raerickson
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@marcosvital Thank you for following up. I will address @MikeKaller's comments. They make sense.

Also, for your information, once I get the review back from the 2nd reviewer, I will need to complete the USGS Review process before returning the final submission to the journal.

@marcosvital
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Thank you for your feedback, @raerickson.

@BrandonEdwards, did you had the chance to start reviewing? Please let us know, ok?

@raerickson
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@marcosvital any updates? Also, would seeing the USGS software review help you?

@marcosvital
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Hi, @raerickson, I'm sorry this is taking so long.

Please, do share with us the USGS software review.

I will try to find an additional reviewer for your submission as fast as possible, so we can finish this.

@marcosvital
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Dear @Cole-Monnahan-NOAA

You answered before about the possibility to review this submission to JOSS. At that time, we had two reviewers, so we started the process with them. Unfortunately one of them could not continue to review, so I would like to know if you are still available.

@raerickson
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raerickson commented Nov 29, 2021 •
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@marcosvital I only have access to one of the two reviews. (They go to a dark archive I do not have access to and I got a new computer this summer).

Here is one of the reviews:
201109 fishStan v2 review - APA.pdf. The reviewer also reviewed an earlier version of the package, where she had more comments (and taught me about linting!).

Also, I have long since deleted the reconciliation branch and my response was also lost for the reasons listed above.

@Cole-Monnahan-NOAA
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@marcosvital yeah I'm still available... please advise on how I should proceed.

@MikeKaller
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MikeKaller commented Nov 30, 2021 via email

@marcosvital
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@marcosvital yeah I'm still available... please advise on how I should proceed.

Thank you, @Cole-Monnahan-NOAA.
I'll add you as a reviewer and guide you through the process.

@marcosvital
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Dear @MikeKaller, thank you for all your work on this submission. Since you have finished your review, there is no need for you to follow this issue anymore, so feel free to turn the notifications off.

@Kevin-Mattheus-Moerman
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@editorialbot generate pdf

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

@Kevin-Mattheus-Moerman
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@raerickson thanks for amending those affiliation descriptions.
About the DOI. I am afraid pointing to the repository is "even worse" (since the repository version is always in flux). The point of archiving the software is such that a non-changing permanent record is maintained of the software. So it should be a static snapshot of the reviewed software and it should be stored permanently. Next the DOI should point to this static/stable long term storage version. It seems like your US government website is not set up for that?
If not, I suggest the following. Download the reviewed software (v2.0.0) and upload it to ZENODO.
Here is an example of such an archived version for a recent JOSS pubication: https://zenodo.org/record/6341565. Note for the ZENODO record the title, and the author list, should match the paper. You make sure you fill in all this meta-data, including the license type, accurately. Once this is completed please report back here with the ZENODO DOI.
Thanks.

@raerickson
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@Kevin-Mattheus-Moerman I have moved the DOI back to the version 2.0 tag https://doi.org/10.5066/P9TT3ILO

The tag is immutable and cannot be changed. The code.usgs.gov page should be stable in the long term. The USGS considers software releases to code.usgs.gov to a formal product type, similar to our data releases on sciencebase.gov, our agencies maps, or our different types of reports.

I am not allowed to create a ZENDO archive because it is not a US Government authorized cloud service.

@raerickson
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@Kevin-Mattheus-Moerman Also, thank you for your patience in working through this!

@raerickson
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@Kevin-Mattheus-Moerman as a bump, any thoughts about this?

@arfon
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arfon commented Mar 21, 2022

@raerickson – JOSS has a strong preference for a service with archiving in it's mission. As such, I've made an archive of the software myself with Zenodo here: 10.5281/zenodo.6373008

In preparing this archive, I noticed a (possibly) bigger challenge, this software is not actually licensed with an OSI-approved license (https://code.usgs.gov/umesc/quant-ecology/fishstan/-/blob/master/LICENSE.md). I'm sorry for not spotting this sooner @raerickson, but CC-0 is not OSI-approved, and as such isn't allowed in JOSS.

I understand that there are reasons US government funded work has guidance for being shared as CC-0, but for other submissions from other US agencies, the authors have been allowed to dual license their submissions.

Calling @kbarnhart and @jedbrown who I believe may have some expertise/experience to share here.

@kbarnhart
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@raerickson this is the best publicly available guidance I've found on what licenses are permitted and/or encouraged for USGS-authored software releases. I've pasted the key text below. In short, of the three licenses listed, only CC0 1.0 is not on the list of OSI approved licenses. In addition, I think that the text could reasonably be interpreted to allow an open-source license other than the three listed.

All software developed by the USGS should by default use an open-source license (put a "LICENSE.md" file in the project root of your repository). Below are license options to consider:

The Creative Commons (CC0) license may be used (currently CC0 1.0) when an official license declaration is required or appropriate to include. This assumes the software is either completely original, or using other software also with the CC0 license. This license places the work as completely as possible in the public domain so that it is free for others to build upon, enhance, or reuse, should work for most USGS software.

"MIT/X11" is an option when governing jurisdictions do not recognize the public domain dedication (e.g. outside the U.S.). Outside the United States, we are not required to release the source unencumbered (though MIT/X11 is probably the least encumbered, open-source license).

The Unlicense (unlicense.org) may be used to opt out of copyright altogether.

@raerickson
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@arfon and @kbarnhart Thank you both of you for helping!

I changed switched to an Unlicense.

I added a sentence to manuscript

An archived version of the package exists on Zenodo (10.5281/zenodo.6373008).

Please let me know if you need me to do anything else.

@danielskatz
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@raerickson - I'm the AEiC on duty this week, so I'm going to do a final proofread/check now

@danielskatz
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.18637/jss.v076.i01 is OK
- 10.1016/j.fishres.2015.03.009 is OK
- 10.1201/9781315371986 is OK
- 10.1002/nafm.10515 is OK
- 10.1002/nafm.10515 is OK
- 10.5066/P9IAOZ8G is OK
- 10.3996/JFWM-20-070 is OK
- 10.5066/P9Q6SUML is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

Check final proof 👉 openjournals/joss-papers#3073

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3073, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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@editorialbot accept

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

@editorialbot
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@editorialbot
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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03444 joss-papers#3074
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03444
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Mar 21, 2022
@danielskatz
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Congratulations to @rerickson-usgs @raerickson and co-authors

And thanks to @MikeKaller and @Cole-Monnahan-NOAA for reviewing, and @marcosvital for editing!
We couldn't do this without you

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🎉🎉🎉 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://joss.theoj.org/papers/10.21105/joss.03444/status.svg)](https://doi.org/10.21105/joss.03444)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03444">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03444/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03444/status.svg
   :target: https://doi.org/10.21105/joss.03444

This is how it will look in your documentation:

DOI

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