PONE-D-24-06375Wild salmon migration routes influence sea lice infestations: An agent-based model predicting farm-related infestations on juvenile salmonPLOS ONE

Dear Dr. Jeong,

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Comments to the Author

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Reviewer #1: Partly

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: No

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Please see uploaded file.

Reviewer #2: Dear Authors,

Thank you for the submission of your manuscript for the publication consideration at PLOS ONE. The manuscript titled "Wild salmon migration routes influence sea lice infestations: An agent-based model predicting farm-related infestations on juvenile salmon" is drafted intelligibly and adhering to scientific principles. Although, the migration and infestation patterns are influenced by various parameters, the simplicity of the model and it's reliance on stochastic modelling eases the interpretation of the results and conclusions derived from it.

There are minor correction I would recommend to improve the manuscript.

1. Re-phrase the sentences

line 26-28 "Specifically, salmon traveling longer migration routes farther from farms may experience higher sea lice loads than those on shorter, farm-adjacent routes"

This sentence may mislead the readers given that the shorter route is already allocated the higher progression rate with zero alpha based on previous studies. The results may only discuss about the progression rate and infestation levels rather than their proximity to farms.

2. Abbreviations

line 58 ABMs -

Avoid plurals in abbreviations

3. Consistency

line 139 and 146

Fraser River and Fraser river

Adhere to one form when indicating the names of the places

4. Syntax

line 145

1st - superscript

line 198

"Details" - Please use the section number along with the section heading

line 339

"British Columbia"

Already defined as BC and yet it has been expanded again

line 552

"sockeye"

Capitalise the first letter of a sentence

I would recommend the authors do a thorough language and syntax checks prior to re-submitting this manuscript.

I am looking forward to read your amended manuscript.

Good luck

Reviwer

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Reviewer #1: Yes: Leif Christian Stige

Reviewer #2: No

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Attachments

Attachment

Submitted filename: Review of manuscript by Jeong et al.pdf

Attachment

Submitted filename: PONE-D-24-06375.pdf

PONE-D-24-06375R1Wild salmon migration routes influence sea lice infestations: An agent-based model predicting farm-related infestations on juvenile salmonPLOS ONE

Dear Dr. Jeong,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

==============================fix things pointed out by reviewer 1.

Please submit your revised manuscript by Aug 17 2024 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Arnar Palsson, Ph.D.

Academic Editor

PLOS ONE

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Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Additional Editor Comments:

Adhere to comments from reviewer 1

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

********** 

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

********** 

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

********** 

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

********** 

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

********** 

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: I find that the authors have addressed all my previous comments nicely.

I have a few additional comments after reading through the text anew.

1) I think the limitations of the infestation model should be clarified better:

- Around L 315 (“lice data”), it should be clarified that the infestation model is based on data on salmon lice Lepeophtheirus salmonis infestations on juvenile Atlantic salmon Salmo salar.

- Around L 625-630, where model limitations are discussed, I think it should be mentioned that to accurate assess the risk in a specific area, it would be necessary with detailed data on spatiotemporal variation in infestation pressure and an infestation model calibrated to observations of Caligus clemensi sea lice on juvenile sockeye salmon Oncorhyncus nerka.

This limitation is not relevant for the conclusions drawn in this paper, but relevant to mention since the model presents the model for the first time, and the purpose of the model as given on L 110-111 seems to open for applying the model for a somewhat wider purpose.

2) I find the text now generally very clear. The explanation on L 376-383 can however be made clearer by explaining that the random draw of values for the four parameters was done jointly, resulting in 3000 simulations where all four parameters varied randomly within the specified ranges.

3) Figure 7 legend needs to explain the difference between A-1 and A-2 etc.

4) L 584-588: An implicit assumption of this argumentation is that lice interfere with one another if their zones overlap, so that a louse has reduced chance of infesting a fish if it is close to another louse. Otherwise, intersecting zones do not reduce the expected number of infestations compared to non-intersecting zones (but the variance is increased). This assumption should be made explicit and the underlying mechanism explained, and if possible supported by references.

5) I noted a few possible minor errors:

L 181: this --> these

L 252: “k and l” --> “l and m”, for consistency with eq. 2?

L 293 – 295: “they” on L 295 does not point back on anything. Rewrite first sentence to start, e.g., with “Price et al demonstrated markedly...”?

L 322: Quotation marks around ‘proportional model’ are missing

L 411: This --> These

L 428: the smaller --> smaller

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

**********

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While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

Wild salmon migration routes influence sea lice infestations: An agent-based model predicting farm-related infestations on juvenile salmon

PONE-D-24-06375R2

Dear Dr. Jeong,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Arnar Palsson, Ph.D.

Academic Editor

PLOS ONE

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