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

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@kavir1698@mikldk<!--end-editor-- Reviewers: @slwu89, @tijeco Archive: 10.5281/zenodo.7303672

Status

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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

editorialbot commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Wordcount for paper.md is 853

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikldk commented 2 years ago

@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 commented 2 years ago

Review checklist for @tijeco

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/kavir1698/EvoDynamics.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

@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 (https://github.com/kavir1698/EvoDynamics.jl/issues/33).

tijeco commented 2 years ago

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 (https://github.com/kavir1698/EvoDynamics.jl/issues/34)

slwu89 commented 2 years ago

Review checklist for @slwu89

Conflict of interest

[x] 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

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

General checks

[x] Repository: Is the source code for this software available at the https://github.com/kavir1698/EvoDynamics.jl?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

@slwu89 Thanks for the update. Get well soon.

slwu89 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikldk commented 2 years ago

@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 commented 2 years ago

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

tijeco commented 2 years ago

@mikldk hoping to finish the review this weekend!

tijeco commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

kavir1698 commented 2 years ago

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 commented 2 years ago

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

mikldk commented 2 years ago

@editorialbot set v0.17.0 as version

editorialbot commented 2 years ago

Done! version is now v0.17.0

mikldk commented 2 years ago

@editorialbot set 10.5281/zenodo.7303672 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.7303672

mikldk commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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 commented 2 years ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3701, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 2 years ago

@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:

[x] You may remove Baltzerstrasse 6, CH-3012 (street postcode info) from the affiliation
[x] 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.
[x] 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 commented 2 years ago

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

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot generate pdf

editorialbot commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 2 years ago

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

Kevin-Mattheus-Moerman commented 2 years ago

@editorialbot accept

editorialbot commented 2 years ago

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

editorialbot commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 2 years ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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 commented 2 years ago

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 commented 2 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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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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