[REVIEW]: EvoDynamics.jl: a framework for modeling eco-evolutionary dynamics #4775

editorialbot · 2022-09-23T07:03:17Z

Submitting author: @kavir1698 (Ali Rezaee Vahdati)
Repository: https://github.com/kavir1698/EvoDynamics.jl
Branch with paper.md (empty if default branch):
Version: v0.17.0
Editor: @mikldk
Reviewers: @slwu89, @tijeco
Archive: 10.5281/zenodo.7303672

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8c79b00b22447e7cab1d4ae295d2ccd8"><img src="https://joss.theoj.org/papers/8c79b00b22447e7cab1d4ae295d2ccd8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8c79b00b22447e7cab1d4ae295d2ccd8/status.svg)](https://joss.theoj.org/papers/8c79b00b22447e7cab1d4ae295d2ccd8)

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

@slwu89 & @tijeco, 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://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mikldk 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 @tijeco

📝 Checklist for @slwu89

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

editorialbot · 2022-09-23T07:03:18Z

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

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

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editorialbot · 2022-09-23T07:03:19Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (746.4 files/s, 109829.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TOML                             4            301              2           1326
Julia                           18            194            238           1254
SVG                              1              1              1            932
XML                              1              0              0            540
Markdown                         8            146              0            390
TeX                              1             11              0            212
YAML                             4              6             22            132
JSON                             2              0              0             31
-------------------------------------------------------------------------------
SUM:                            39            659            263           4817
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-09-23T07:03:20Z

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

OK DOIs

- 10.1038/nrg.2016.58 is OK
- 10.1093/bioinformatics/bty197 is OK
- 10.1016/j.mex.2020.100978 is OK
- 10.1016/j.tree.2018.04.009 is OK
- 10.1126/science.1193954 is OK
- 10.1111/j.1461-0248.2010.01545.x is OK
- 10.1038/s41576-021-00394-0 is OK
- 10.1002/bes2.1801 is OK
- 10.1098/rstb.2009.0012 is OK
- 10.1093/bioinformatics/btz311 is OK
- 10.1093/bioinformatics/btl415 is OK
- 10.1186/s12859-021-04415-x is OK
- 10.1111/ecog.05687 is OK
- 10.1093/molbev/msw211 is OK
- 10.1111/ecog.00680 is OK
- 10.1177/00375497211068820 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-09-23T07:03:20Z

Wordcount for paper.md is 853

editorialbot · 2022-09-23T07:04:54Z

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

mikldk · 2022-09-23T07:05:09Z

@slwu89, @tijeco: Thanks for agreeing to review. Please carry out your review in this issue by first creating a checklist (@editorialbot generate my checklist) and then updating it as the review proceeds. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

tijeco · 2022-09-24T13:02:10Z

Review checklist for @tijeco

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

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

General checks

Repository: Is the source code for this software available at the https://github.com/kavir1698/EvoDynamics.jl?
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 (@kavir1698) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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)?
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, who the target audience is, and its relation to other work?
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?

tijeco · 2022-09-24T15:07:02Z

@kavir1698 I've started going through the examples. I started with the following agentdata, modeldata, model = runmodel("examples/paramfile1.jl") and ran into an error, which I believe is due to a typo in the paramfile. I've raised an issue here (kavir1698/EvoDynamics.jl#33).

tijeco · 2022-09-24T15:25:31Z

As is, the example in examples/paramfile2.jl works as expected. I'd say the documentation on setting up the model parameters and running the simulations is well done, but there seems to be very little on the interpretation of what the output is.

For example, the runmodel() function that is used to create agentdata, modeldata, model, a dataframe with values mean_fitness_per_species and species_N is generated, but I see no description of what those fields are in the documentation.

I think the documentation of the expected output needs to be updated. I've submitted an issue with more information here (kavir1698/EvoDynamics.jl#34)

slwu89 · 2022-09-25T17:42:56Z

Review checklist for @slwu89

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

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

General checks

Repository: Is the source code for this software available at the https://github.com/kavir1698/EvoDynamics.jl?
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 (@kavir1698) 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
Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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)?
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, who the target audience is, and its relation to other work?
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?

kavir1698 · 2022-09-26T11:56:02Z

Thank you @tijeco for your feedback. I have addressed the issue. Once all the issue of this review are addressed, I will release a new version of the package.

slwu89 · 2022-10-06T22:28:37Z

Hi @mikldk, I've been rather sick lately and unable to start the review yet. I'll aim to begin next week, I just wanted to update here to let you know I'm aware of the task.

mikldk · 2022-10-07T07:02:01Z

@slwu89 Thanks for the update. Get well soon.

slwu89 · 2022-10-13T17:52:09Z

@editorialbot generate pdf

editorialbot · 2022-10-13T17:53:58Z

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

mikldk · 2022-10-24T12:39:11Z

@tijeco: Can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

@slwu89: Can you confirm that you have finished the review and recommend that this paper is now published?

slwu89 · 2022-10-25T22:56:19Z

@mikldk yes, all of my comments have been addressed in a satisfactory manner and I recommend publication.

tijeco · 2022-10-26T19:37:16Z

@mikldk hoping to finish the review this weekend!

tijeco · 2022-11-04T01:25:40Z

@mikldk and @kavir1698 I've finished my review! This is a really awesome library, and I'm excited to see the many fun studies that come out that use this library!

I definitely recommend publication.

mikldk · 2022-11-04T09:20:16Z

@slwu89, @tijeco: Thanks for the reviews! And for the recommendation of publication.

@kavir1698 :

Please have a final read though of the paper, checking language etc.
Have a final check of the proofs with @editorialbot generate pdf
In general, be sure that all versions are correct and that the repo is in the state that should be published.
Please make a tagged release and archive (e.g. with Zenodo) as described here, and report the version number and archive DOI in this thread. Please verify that the archive deposit has the correct metadata (title and author list), or edit these if that is not the case.

kavir1698 · 2022-11-08T09:48:59Z

@editorialbot generate pdf

editorialbot · 2022-11-08T09:50:38Z

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

kavir1698 · 2022-11-08T10:26:26Z

Thank you all for your time.

@mikldk The version of the package to the published is v0.17.0 (https://zenodo.org/record/7303672). The DOI is 10.5281/zenodo.7303672.

kavir1698 · 2022-11-08T10:49:44Z

Can I update the version mentioned in the paper from 0.16.0 to 0.17.0?

mikldk · 2022-11-09T14:40:34Z

@editorialbot set v0.17.0 as version

editorialbot · 2022-11-09T14:40:35Z

Done! version is now v0.17.0

mikldk · 2022-11-09T14:40:58Z

@editorialbot set 10.5281/zenodo.7303672 as archive

editorialbot · 2022-11-09T14:41:00Z

Done! Archive is now 10.5281/zenodo.7303672

mikldk · 2022-11-09T14:41:29Z

@editorialbot recommend-accept

editorialbot · 2022-11-09T14:41:31Z

Attempting dry run of processing paper acceptance...

editorialbot · 2022-11-09T14:41:33Z

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

OK DOIs

- 10.1038/nrg.2016.58 is OK
- 10.1093/bioinformatics/bty197 is OK
- 10.1016/j.mex.2020.100978 is OK
- 10.1016/j.tree.2018.04.009 is OK
- 10.1126/science.1193954 is OK
- 10.1111/j.1461-0248.2010.01545.x is OK
- 10.1038/s41576-021-00394-0 is OK
- 10.1002/bes2.1801 is OK
- 10.1098/rstb.2009.0012 is OK
- 10.1093/bioinformatics/btz311 is OK
- 10.1093/bioinformatics/btl415 is OK
- 10.1186/s12859-021-04415-x is OK
- 10.1111/ecog.05687 is OK
- 10.1093/molbev/msw211 is OK
- 10.1111/ecog.00680 is OK
- 10.1177/00375497211068820 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-11-09T14:43:16Z

👋 @openjournals/bcm-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/joss-papers#3701, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman · 2022-11-14T22:31:11Z

@kavir1698 I am the AEiC for this track and here to help process this work for acceptance in JOSS. I have check the ZENODO archive and all seems in order there. I have read your paper too and have the below remaining points that need your attention, feel free to disagree with some of these recommendations:

You may remove Baltzerstrasse 6, CH-3012 (street postcode info) from the affiliation
Consider rephrasing this sentence: EvoDynamics.jl aims to connect genomes and phenomes in an easy building-block way to allow exploring many scenarios connecting the two.. In particular the in an easy building-block way sounds awkward, and allow exploring many scenarios connecting the two should perhaps become something like enabling the exploration of many scenarios connecting the two.
Perhaps, unless I misunderstood, ...for biodiversity response to global change... should read ...for biodiversity responses to global change...

Let me know when you've processed the above. Thanks.

kavir1698 · 2022-11-16T10:57:46Z

Hi @Kevin-Mattheus-Moerman,
Thanks for your feedback. I have incorporated your suggestions in the paper.

Kevin-Mattheus-Moerman · 2022-11-16T11:15:36Z

@editorialbot generate pdf

editorialbot · 2022-11-16T11:16:51Z

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

Kevin-Mattheus-Moerman · 2022-11-16T14:15:03Z

@kavir1698 all looks good to me now. Thanks for processing those changes. We will proceed now with formal acceptance.

Kevin-Mattheus-Moerman · 2022-11-16T14:15:10Z

@editorialbot accept

editorialbot · 2022-11-16T14:15:12Z

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

editorialbot · 2022-11-16T14:16:52Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2022-11-16T14:16:53Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04775 joss-papers#3728
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04775
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman · 2022-11-16T15:37:42Z

Congratulations @kavir1698 on this JOSS publication!!!!

And thank you @mikldk for editing!

Also a special thank you to @slwu89 and @tijeco for their review efforts!

editorialbot · 2022-11-16T15:37:44Z

🎉🎉🎉 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:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04775/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04775/status.svg
   :target: https://doi.org/10.21105/joss.04775

This is how it will look in your documentation:

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editorialbot added Julia review TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Sep 23, 2022

editorialbot assigned mikldk Sep 23, 2022

editorialbot mentioned this issue Sep 23, 2022

[PRE REVIEW]: EvoDynamics.jl: a framework for modeling eco-evolutionary dynamics #4750

Closed

This was referenced Oct 9, 2022

Error in Wright-Fisher example kavir1698/EvoDynamics.jl#35

Closed

Suggestions for JOSS paper language kavir1698/EvoDynamics.jl#36

Closed

Exported function documentation kavir1698/EvoDynamics.jl#37

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 9, 2022

editorialbot added accepted published Papers published in JOSS labels Nov 16, 2022

Kevin-Mattheus-Moerman closed this as completed Nov 16, 2022

editorialbot mentioned this issue Aug 7, 2024

[PRE REVIEW]: Mango.jl: A Julia-Based Multi-Agent Simulation Framework #7083

Closed

editorialbot mentioned this issue Sep 16, 2024

[PRE REVIEW]: Mozzie: a computationally efficient simulator for the spatio-temporal modelling of mosquitoes #7230

Closed

[REVIEW]: EvoDynamics.jl: a framework for modeling eco-evolutionary dynamics #4775

[REVIEW]: EvoDynamics.jl: a framework for modeling eco-evolutionary dynamics #4775

Comments

editorialbot commented Sep 23, 2022 • edited Loading

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Reviewer instructions & questions

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mikldk commented Sep 23, 2022

tijeco commented Sep 24, 2022 • edited Loading

Review checklist for @tijeco

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

tijeco commented Sep 24, 2022

tijeco commented Sep 24, 2022

slwu89 commented Sep 25, 2022 • edited Loading

Review checklist for @slwu89

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

kavir1698 commented Sep 26, 2022

slwu89 commented Oct 6, 2022

mikldk commented Oct 7, 2022

slwu89 commented Oct 13, 2022

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mikldk commented Oct 24, 2022

slwu89 commented Oct 25, 2022

tijeco commented Oct 26, 2022

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kavir1698 commented Nov 8, 2022

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Kevin-Mattheus-Moerman commented Nov 14, 2022 • edited Loading

kavir1698 commented Nov 16, 2022

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