[REVIEW]: Viable North Sea (ViNoS): A NetLogo Agent-based Model of German Small-scale Fisheries

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@platipodium@marcosvital<!--end-editor-- Reviewers: @nick-gauthier, @Fabbiologia, @changliao1025 Archive: 10.5281/zenodo.7928199

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/84a737c77c6d676d0aefbcef8974b138"><img src="https://joss.theoj.org/papers/84a737c77c6d676d0aefbcef8974b138/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/84a737c77c6d676d0aefbcef8974b138/status.svg)](https://joss.theoj.org/papers/84a737c77c6d676d0aefbcef8974b138)

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

@nick-gauthier & @Fabbiologia & @changliao1025, 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 @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 ✨

Checklists

📝 Checklist for @Fabbiologia

📝 Checklist for @changliao1025

📝 Checklist for @nick-gauthier

editorialbot commented 1 year ago

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:

@editorialbot commands

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

@editorialbot generate pdf

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (779.1 files/s, 127502.7 lines/s)
---------------------------------------------------------------------------------------
Language                             files          blank        comment           code
---------------------------------------------------------------------------------------
TeX                                      9            517            452           4111
XML                                      8              0             15           3029
Markdown                                24            560              0           1589
Python                                   9            224            116            631
YAML                                     9             21             82            278
make                                     9             82             49            189
JSON                                     1              0              0            115
HTML                                     1              1              5             85
R                                        2             14             14             63
Rmd                                      1             38             35             49
TOML                                     1              4              3             29
CSS                                      1              4              5             20
Windows Module Definition                1              1              0              7
---------------------------------------------------------------------------------------
SUM:                                    76           1466            776          10195
---------------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1141

editorialbot commented 1 year ago

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

OK DOIs

- 10.1201/9781351106252 is OK
- 10.1016/j.ecolmodel.2010.08.019 is OK
- 10.18564/jasss.4259 is OK
- 10.1007/978-3-319-43884-9_13 is OK
- 10.1016/j.ocecoaman.2023.106543 is OK
- 10.1007/978-3-030-37371-9_23 is OK
- 10.1016/j.marpol.2021.104675 is OK
- 10.1007/s10618-019-00646-y is OK
- 10.17895/ices.pub.8105 is OK

MISSING DOIs

- 10.1111/j.1365-2664.2008.01488.x may be a valid DOI for title: Climate change and deepening of the North Sea fish assemblage: a biotic indicator of warming seas
- 10.1016/j.rser.2022.112108 may be a valid DOI for title: From plate to plug: the impact of offshore renewables on European fisheries and the role of marine spatial planning
- 10.1111/j.1365-2664.2008.01488.x may be a valid DOI for title: Climate change and deepening of the North Sea fish assemblage: a biotic indicator of warming seas
- 10.1093/icesjms/fsaa050 may be a valid DOI for title: Different bottom trawl fisheries have a differential impact on the status of the North Sea seafloor habitats
- 10.17487/rfc4180 may be a valid DOI for title: Common Format and MIME Type for Comma-Separated Values (CSV) Files
- 10.17487/rfc4180 may be a valid DOI for title: Common Format and MIME Type for Comma-Separated Values (CSV) Files

INVALID DOIs

- None

editorialbot commented 1 year ago

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

marcosvital commented 1 year ago

Dear @nick-gauthier, @Fabbiologia and @changliao1025, thank you again for accepting review this submission for JOSS. The reviewing process is checklist based, and instructions were already posted above by the editorial bot - but let me know if you need any assistance, ok? Also, you can tag @platipodium if you have specific questions about the manuscript.

@platipodium, you can tag any of your co-authors GitHub accounts if you want, so they will be able to follow this issue. In the meantime, also please take a look at the 'missing DOIs' detected by the editorial bot. You can generate a new pdf version of the manuscript if you make any changes.

Fabbiologia commented 1 year ago

Review checklist for @Fabbiologia

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://codebase.helmholtz.cloud/mussel/netlogo-northsea-species.git?
[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 (@platipodium) 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] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[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?

platipodium commented 1 year ago

Thanks @nick-gauthier @Fabbiologia @changliao1025 for agreeing to review my submission.

platipodium commented 1 year ago

Created an issue for completing missing doi at https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/71

Checklist for author @platipodium:

[x] missing DOI completed (check once done)
[x] tag co-author's GitHub addresses (note: the dev is on gitlab, so not all authors have a GitHub account)

platipodium commented 1 year ago

@marcosvital please ask @editorialbot to update the version to 1.1.0

platipodium commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1201/9781351106252 is OK
- 10.1016/j.ecolmodel.2010.08.019 is OK
- 10.18564/jasss.4259 is OK
- 10.1007/978-3-319-43884-9_13 is OK
- 10.1016/j.ocecoaman.2023.106543 is OK
- 10.1111/j.1365-2664.2008.01488.x is OK
- 10.1016/j.rser.2022.112108 is OK
- 10.1007/978-3-030-37371-9_23 is OK
- 10.1016/j.marpol.2021.104675 is OK
- 10.1007/s10618-019-00646-y is OK
- 10.17895/ices.pub.8105 is OK
- 10.1093/icesjms/fsaa050 is OK
- 10.17487/rfc4180 is OK

MISSING DOIs

- None

INVALID DOIs

- None

platipodium commented 1 year ago

Tagging co-authors

@s-orey
@saho1234
(one still missing)

platipodium commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

platipodium commented 1 year ago

github.com/AlDanial/cloc v 1.88 T=0.10 s (779.1 files/s, 127502.7 lines/s)

JOSS's cloc version 1.88 does not yet account for NetLogo. You can executed make -C netlogo cloc in the projects's root dir to obtain the correct NetLogo count:

github.com/AlDanial/cloc v 1.97  T=0.01 s (1300.5 files/s, 329133.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
NETLOGO                         13            553            336           2401

marcosvital commented 1 year ago

@editorialbot set 1.1.0 as version

editorialbot commented 1 year ago

Done! version is now 1.1.0

platipodium commented 1 year ago

Current version is now 1.2.0., please @marcosvital bump the version in editorialbot

platipodium commented 1 year ago

Dear @nick-gauthier @changliao1025 you have not started your review. Is there an accessibility issue that I should resolve to make it easier to obtain/download/run the software?

Fabbiologia commented 1 year ago

Hi! @platipodium, I have some suggestions and issues to discuss, but can't create a formal issue on the GitLab page as it requires an institutional login, or am i doing something wrong?

My personal GitLab credentials don't work. I believe i am supposed to create formal issues to complete the review checklist, correct? @marcosvital

platipodium commented 1 year ago

Thanks @Fabbiologia.

Indeed, the login page is quite confusing (but that is outside our control)
Yes, you need to authenticate (and then sign in) to create issues. This is not your personal gitlab instance or gitlab.com instance's login, but can be any of your uni/academic institution/github/orcid ... authentication provider, see below.
There is a description in the section "Contributing and reporting" at the bottom of the Readme.md:

To file an issue or to contribute, you are asked (1) to authenticate and (2) to register: When asked, scroll all the way down and click Sign in with Helmholtz AAI. On the following page "Login to Helmholtz AAI OAuth2 Authorization Server", search for one of your existing authentication providers (this may be your university, company, ORCID, github, or many others) and log in. You are then asked to provide name and email address for registration on the HIFIS GitLab instance.

Please report (here) if those instructions are clear enough for you to authenticate and sign in to create issues. If not, I'd have to improve those instructions.

Fabbiologia commented 1 year ago

Got it! I requested access through github, don't know why it did not worked through University authorization portal. Thank you for the info!

Fabbiologia commented 1 year ago

I believe the model is great and holds tremendous potential. Congratulations to the team for the work accomplished thus far.

However, I have some suggestions that could enhance both the Graphical User Interface (GUI) and the software's outputs:

GUI Documentation: Although I may have overlooked it, I was unable to locate a comprehensive guide detailing the functions of each GUI button (I am sorry if it is there, I am very bad at finding things). While the buttons are largely self-explanatory, a visual manual delineating each action and its expected impact on the model would be beneficial for a broader user base.
Clarification on Final Outputs: Could you specify the expected final outputs of the model and their intended applications? Are users expected to interpret these outputs visually? A descriptive commentary accompanying an example run would be important in guiding users through what they are expected to observe, execute, and interpret. While I understand that training may easily address this, a practical guide would be a worthwhile addition.

These suggestions pertain to my review criteria, which include:

Example Usage: Do the authors provide examples illustrating how to utilize the software, ideally to address real-world analytical challenges?
Summary: Is there a lucid description of the software's high-level functionality and purpose, aimed at a diverse, non-specialist audience?

I believe there is still room for improvement in these areas.

In summary, the software is commendable, and I would recommend it for publication once these adjustments have been implemented or clarified.

platipodium commented 1 year ago

Thanks @Fabbiologia, I split up your issue in two on our gitlab, they are

[x] Output clarification: https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/88
[ ] GUI documentation: https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/87

Also, you noticed a warning

[x] https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/85

Fabbiologia commented 1 year ago

Hello @marcosvital,

I have reviewed the manuscript and evaluated the model, which is based on robust assumptions and has been ground-truthed where feasible. The software installs seamlessly and functions without issues across various platforms. Although there is a Java-related issue on macOS, the authors have proactively addressed it by providing anticipatory instructions. I am satisfied with the responses they have offered to a few concerns I raised—more in the form of suggestions rather than corrections. Consequently, I recommend the software for publication.

marcosvital commented 1 year ago

Thank you very much for reviewing and contributing with this submission, @Fabbiologia.

marcosvital commented 1 year ago

@nick-gauthier @changliao1025, I see that you didn't created your checklist yet. Let us know if you are still available to review this submission and if need any assistance, ok?

platipodium commented 1 year ago

Current version is now 1.2.1. @marcosvital you may bump the version number. Development in upcoming version 1.2.2 will contain elaborations on @Fabbiologia's suggestions to improving the UX.

changliao1025 commented 1 year ago

Review checklist for @changliao1025

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://codebase.helmholtz.cloud/mussel/netlogo-northsea-species.git?
[ ] 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 (@platipodium) 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?
[ ] 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)?
[x] 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

[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?

platipodium commented 1 year ago

@editorialbot generate pdf

nick-gauthier commented 1 year ago

Review checklist for @nick-gauthier

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://codebase.helmholtz.cloud/mussel/netlogo-northsea-species.git?
[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 (@platipodium) 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?

platipodium commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

changliao1025 commented 1 year ago

I am still awaiting the account approval to post issues on the repository.

platipodium commented 1 year ago

I am still awaiting the account approval to post issues on the repository.

Dear @changliao1025 . There is no account approval necessary. It is

authorisation with one of your digital identities
self-registration
login

Please post problems with registering and logging in here.

changliao1025 commented 1 year ago

I encountered some technical issues with the registration; see the screenshot:

changliao1025 commented 1 year ago

I tried to use my GitHub credential to register fyi.

platipodium commented 1 year ago

Thanks @changliao1025 . I could reproduce the steps you described, registering myself anew with my GitHub credentials (I usually use my university one). After the page you screenshotted "Registration request submitted", I obtained an email to my email account registered as primary on Github:

Bildschirmfoto 2023-10-05 um 09 33 24

I then could confirm by clicking the link. I proceeded to accept access of the GitLab HIFIS to my GitHub account and the registration process completed.

Please check your SPAM folder or alternate email inbox for the confirmation mail that seemed to have been lost.

@nick-gauthier how did you fare with registering on the GitLab instance?

changliao1025 commented 1 year ago

I fixed it. I think the email went to junk earlier, and I couldn't find it for some reason. I will continue with the review.

platipodium commented 1 year ago

I fixed it. I think the email went to junk earlier, and I couldn't find it for some reason. I will continue with the review.

To improve the process, I amended the Readme.md as follows:

If you are not already registered on the HIFIS GitLab instance, a confirmation email will be sent to the primary email address registered with your authentication provider. After clicking the confirmation link, you will also be asked to provide a name on this Gitlab instance; this will be your nickname.

platipodium commented 1 year ago

@changliao1025 created two issues

Let's tick them off once they're resolved upstream. Thanks for reporting.

platipodium commented 11 months ago

Dear @marcosvital please bump version to 1.2.3

Latest LOC report is

github.com/AlDanial/cloc v 1.99  T=0.02 s (874.0 files/s, 241377.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
NETLOGO                         17            794            546           3355
-------------------------------------------------------------------------------

marcosvital commented 11 months ago

@editorialbot set 1.2.3 as version

editorialbot commented 11 months ago

Done! version is now 1.2.3

changliao1025 commented 11 months ago

General checks

[x] Repository: I am able to access the repository now.
[ ] License: I already opened an issue for this.
[x] Contribution and authorship: I am unable to open the contributor statistics from the repo: https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/graphs/main?ref_type=heads. But the repo contains a section about the contribution.
[x] Substantial scholarly effort: Yes.
[x] Data sharing: It appears there are large datasets saved as csv or GeoTiff formats. And there is not clear description how they are used in the documentation. Although the authors provide some instruction on where to download the data, it is unclear how to pre-process them. But since this model intends to be only applied to one region/domain, I think this is not a big issue.
[x] Reproducibility: I was able to run the model on both mac and Windows. But as the paper stated some process uses random approach to define direction, then the model may not be able to produce the same result in different runs.
[x] Human and animal research: No data associated with human and animal research.

Functionality

[x] Installation: The model mainly use the NetLogo as the host. So installation is relatively straightforward.
[x] Functionality: Yes.
[x] Performance: This is a GUI-based model, and it depends on NetLogo, so I think its performance depends on the NetLogo?

Documentation

[x] A statement of need: I don't quite understand the application of this model since there are a couple of limitations. 1) if the steps are randomly generated, then should this be used a guidance or it should be treated as a scenario emulator? For example, the purpose this model is to find the best location for fishing, then should it implement some optimization scheme instead of using a random approach? I might have misunderstood something, correct me if I am wrong about the details.
[x] Installation instructions: The NetLogo installation is mentioned.
[x] Example usage: The model uses a domain-based datasets, so it is close to a real world problem.
[ ] Functionality documentation: Since everything is carried out in NetLogo, users are not exposed to APIs. Instead, users can use the NetLogo buttons, choosers, to adjust the model parameters. I found there are some Python/R scripts in the repo, but I could not find documentation how they are used.
[x] Automated tests: I could not find any test information. There is also no figures in the paper. A animation of the model run would be helpful.
[x] Community guidelines: Yes.

Software paper

[x] Summary: Summary is OK in the current format.
[x] A statement of need: Generally clear. But I think the currently functionality may need improvement for those purposes.
[x] State of the field: I couldn't find a section for this.
[x] Quality of writing: The writing is easy to understand.
[ ] References:

platipodium commented 11 months ago

General checks

[x] Repository: I am able to access the repository now.

[ ] License: I already opened an issue for this.

This is documented in https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/101, thanks @changliao1025

I addressed the license grouping request, added OSI statement and labelled the different licenses with the OSI logo where applicable. Is this sufficiently addressed?

platipodium commented 11 months ago

General checks

[x] Contribution and authorship: I am unable to open the contributor statistics from the repo: https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/graphs/main?ref_type=heads. But the repo contains a section about the contribution.

I created an issue over at https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/115 . The contributor stats is not available if you don't have developer status on that repo. I pasted a snapshot of today's gitstats dump in the issue.

platipodium commented 11 months ago

[x] Data sharing: It appears there are large datasets saved as csv or GeoTiff formats. And there is not clear description how they are used in the documentation. Although the authors provide some instruction on where to download the data, it is unclear how to pre-process them. But since this model intends to be only applied to one region/domain, I think this is not a big issue.

Thanks for pointing this out. Yes, we use a large amount of external data, all available as open data, but not in suitable formats to be ingested into NetLogo. So we preprocess the data and provide it in the repository in the format suitable for running the model. I opened a feature request to elaborate on this process https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/116

platipodium commented 11 months ago

[x] Reproducibility: I was able to run the model on both mac and Windows. But as the paper stated some process uses random approach to define direction, then the model may not be able to produce the same result in different runs.

This is now a feature request in https://codebase.helmholtz.cloud/mussel/netlogo-northsea-species/-/issues/117

openjournals / joss-reviews