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[PRE REVIEW]: fishStan: Hierarchical Bayesian models for fisheries #3117

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whedon opened this issue Mar 16, 2021 · 49 comments
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[PRE REVIEW]: fishStan: Hierarchical Bayesian models for fisheries #3117

whedon opened this issue Mar 16, 2021 · 49 comments
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@marcosvital @BrandonEdwards
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C++ pre-review R Stan

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@whedon
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whedon commented Mar 16, 2021 •
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Submitting author: @rerickson-usgs (Richard Erickson)
Repository: https://code.usgs.gov/umesc/quant-ecology/fishstan/
Version: v2.0
Editor: @marcosvital
Reviewers: @BrandonEdwards , @MikeKaller
Managing EiC: Arfon Smith

⚠️ 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.

Author instructions

Thanks for submitting your paper to JOSS @rerickson-usgs. Currently, there isn't an JOSS editor assigned to your paper.

@rerickson-usgs if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
@whedon
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whedon commented Mar 16, 2021

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

⚠️ 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.

For a list of things I can do to help you, just type:

@whedon commands

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

@whedon generate pdf

@whedon
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whedon commented Mar 16, 2021 

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.13 s (478.7 files/s, 39316.7 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 'd471026504b4f63c4ce35355' was
gathered on 2021/03/16.
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 Mar 16, 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 Mar 16, 2021

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

@arfon arfon added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 16, 2021
@arfon
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arfon commented Mar 16, 2021

@rerickson-usgs - many thanks for your review here. Unfortunately the editor best-placed to edit this submission is currently very busy so I'm going to add this to the backlog of 'waitlisted' submissions. Hopefully this won't be too long.

@raerickson
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@arfon I hope you're doing well. Do you have any idea when my submission might move off the waitlist?

@arfon
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arfon commented Apr 23, 2021

@whedon invite @marcosvital as editor

👋 @marcosvital - would you be able to handle this submission for us?

@whedon
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whedon commented Apr 23, 2021

@marcosvital has been invited to edit this submission.

@marcosvital
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Hi, @arfon! Yes, I can handle this submission.

@marcosvital
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@whedon assign @marcosvital as editor

@whedon
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whedon commented Apr 27, 2021

OK, the editor is @marcosvital

@marcosvital
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Hi, @rerickson-usgs, I will be the editor of your submission.

Please take a look at the manuscript proof generated above, and check if it seems ok. If you make any changes or corrections on it you can use the command @whedon generate pdf to create a new version (or just let me know and I'll do it).

At the same time, we can start assigning reviewers for you submission. We usually ask the authors for suggestions, so let me know if you have anyone in mind that could do this - you can paste the github profile of anyone you think that could do it (but please don't tag anyone yet).
You can also check this list of people that have agreed to review for JOSS, and see if any of them may be suitable to review this submission.

@marcosvital marcosvital removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Apr 27, 2021
@raerickson
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@marcosvital Thank you for getting back to me and sorry for my delayed response. I'm working part-time because I am on paternity leave.

Here are possible reviewers:

From you list (in my order guessed best fit):

  • trashbirdecology because they do Ecology and R and I've seen some of their work on GitHub and recognize their user name
  • vbaliga because they do R-packages and ecology
  • ha0yebe because they do ecology and R
  • mdogucu because they do Bayesian statistics and R

Please let me know if you need more reviewer suggestions. I know it can be hard to find reviewers.

@raerickson
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raerickson commented May 11, 2021 •
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@marcosvital or @arfon Do you need anything else from me?

@marcosvital
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Hi, @rerickson-usgs! Sorry about the long delay. I'll check your suggestions and start inviting right away.

@marcosvital
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Dear @mbjoseph, @OliverFishCode and @jsta, would you be willing to review this submission for JOSS?

We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission.

@OliverFishCode
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OliverFishCode commented May 12, 2021 via email

@marcosvital
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Thank you for leting us know, @OliverFishCode

@marcosvital
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Dear @mdogucu, would you be willing to review this submission for JOSS?

We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission.

@mdogucu
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mdogucu commented May 14, 2021

I am not available to review at this time, unfortunately.

@marcosvital
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Thank you for your quick reply, @mdogucu!

@marcosvital
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Dear @BrandonEdwards and @becarioprecario, would you be willing to review this submission for JOSS?

We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission.

@becarioprecario
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becarioprecario commented May 18, 2021 via email

@whedon
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whedon commented May 19, 2021

OK, @BrandonEdwards is now a reviewer

@marcosvital
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Hi, @rerickson-usgs! I tried to contact two additional reviewers by email. I'll wait a few days to hear from them, and will continue to search for more potential reviewers depending on their responses ok?

@raerickson
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@marcosvital Thanks. Please let me know if you any more name. Also, somewhere I suggested several people in a different JOSS issue.

@OliverFishCode
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OliverFishCode commented May 27, 2021 via email

@marcosvital
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If you need reviewer recommendations I could also provide some as I was able to review myself. - Devon
…
On Thu, May 27, 2021 at 6:48 AM Richard Erickson @.***> wrote: @marcosvital https://github.com/marcosvital Thanks. Please let me know if you any more name. Also, somewhere I suggested several people in a different JOSS issue. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3117 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AI2HT2COYVLQJZ33GXXTVFDTPZERVANCNFSM4ZI7BYRQ .

Hi, @OliverFishCode! Some recommendations would be great, thank you!

@rerickson-usgs, unfortunately I've got no responses from the emails I sent... I'll keep trying to find additional reviewers, ok?

@OliverFishCode
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OliverFishCode commented Jun 7, 2021 via email

@raerickson
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@marcosvital if you are having trouble after that list, please let me know and I would be a happy to post on the Stan User Forum.

@marcosvital
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marcosvital commented Jun 11, 2021 •
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The following people would be good reviewer choices in no particular order. Mathew Clement @.*** Bill Hintz @.*** Alison Coulter @.*** Michael Kaller @.*** On Mon, Jun 7, 2021, 1:31 PM Marcos Vital (LEQ-UFAL) < @.***>

@OliverFishCode, can you send me their contact information? I'll try to reach them. You can send me by email: marcosvital at gmail.com

@marcosvital
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@marcosvital if you are having trouble after that list, please let me know and I would be a happy to post on the Stan User Forum.

Thank you, @rerickson-usgs! Let's wait to see if one of the recommendations above will work, ok?

@raerickson
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@marcosvital do you need any more recommendations?

@marcosvital
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Hi, @rerickson-usgs! I'm sorry about how long this is taking...
I've contact new possible reviewers by email, and hope they will answer soon. While we wait a little longer, please let me know of any other possible reviewers you have in mind, as I can try to reach them if I don't get any of the responses I'm waiting for.

@raerickson
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https://github.com/bob-carpenter from the Stan project

https://betanalpha.github.io/writing/

@raerickson
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Two more people

https://github.com/bbolker

https://github.com/dmbates

@marcosvital
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Dear @bob-carpenter, would you be willing to review this submission for JOSS?

We carry out an open checklist-driven reviews here in GitHub issues, and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

This is still a pre-review issue, and once there are enough reviewers we will move on to a new issue where the review will take place. If you are not able to review, please let us know if you have recommendations for other reviewers that could help with this submission.

@marcosvital
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@MikeKaller agreed to review this submission.

@marcosvital
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@whedon add @MikeKaller as reviewer

@whedon
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whedon commented Jul 2, 2021

OK, @MikeKaller is now a reviewer

@marcosvital
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Dear @rerickson-usgs, once again, I'm sorry it took so long to move from this pre-review to a active reviewing stage. Usually, we would prefer to have three reviewers, but since it has been challenging to find additional reviewers for this particular submission, we will move on with two.

@BrandonEdwards and @MikeKaller, thank you very much for agreeing to review this submission at JOSS. We will now move to a new GitHub issue that will be dedicated to the reviewing process. Please feel free to contact me at any stage if you need any assistance or clarification, ok?

@marcosvital
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@whedon start review

@whedon
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whedon commented Jul 2, 2021

OK, I've started the review over in #3444.

@whedon whedon closed this as completed Jul 2, 2021
@bob-carpenter
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Thanks for inviting me. I read through your checklist of reviewing requirements and think they're great. But I'm not going to have time to carry out such a thorough review. I am happy to answer specific questions about the usage of Stan or about Bayesian modeling and will see pings or answer emails.

Another good person to ask would be @colemonnahan --- he's a fisheries scientist and knows Stan and its algorithms very well; see his review paper on HMC for ecology.

@Cole-Monnahan-NOAA
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@bob-carpenter is right that I do seem well-placed to review this package.

I'm not familiar with JOSS reviews so not sure exactly what is going on here. Please provide more info as you see fit.

Also for arcane US gov't reasons I now have to use the tag @Cole-Monnahan-NOAA

@raerickson
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raerickson commented Jul 6, 2021 via email

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