Peer Review History

Original SubmissionSeptember 15, 2023
Decision Letter - Md. Naimur Rahman, Editor

PONE-D-23-30056Quantifying the topographical structure of rough seabedsPLOS ONE

Dear Dr. Sous,

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.

Please submit your revised manuscript by Mar 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,

Md. Naimur Rahman

Academic Editor

PLOS ONE

Journal Requirements:

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We will update your Data Availability statement on your behalf to reflect the information you provide.

6. We note that Figures 1-6 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

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Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

7. 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:

Dear Authors,

Thank you for submitting your manuscript to our journal. We have completed the review process, and I have carefully considered the feedback provided by the reviewers and my own reading of your paper.

Your study presents a comprehensive multi-site analysis of high-resolution topography surveys in rough nearshore environments, with the objective of identifying relevant metrics for quantifying the geometrical structure of seabeds. The use of advanced ANN models combined with remote sensing data in your methodology is commendable and represents a significant step forward in geomorphological research.

However, there are several areas that require attention before your manuscript can be considered for publication:

1. **Introduction and Contextualization**: The introduction needs to be expanded to better situate the study within the existing body of literature. It should clearly articulate the research gaps your study aims to address. Please ensure that both historical and recent relevant studies are cited to demonstrate the evolution of the field and to justify the need for your research.

2. **Methodological Details**: While your methodology is robust, greater detail is required to ensure reproducibility. Specifics on data collection, processing, and analysis should be expanded. Please consider including supplementary material if necessary to accommodate additional methodological explanation.

3. **Statistical Analysis**: The statistical approach used to identify relevant roughness metrics needs a more detailed explanation. The choice of metrics and their computation warrants further elaboration. Furthermore, a discussion on the implications of choosing different metrics would be beneficial to the reader.

4. **Results Presentation**: The results section would benefit from additional figures and tables that synthesize the key findings. Visual representations of the data can greatly enhance the readability and impact of your results.

5. **Discussion**: The discussion could be strengthened by directly linking the study's findings to the implications for regional planning and mitigation strategies. Additionally, the potential limitations of the study and directions for future research should be more thoroughly discussed.

6. **Conclusion**: The conclusion should succinctly summarize the main findings, their significance, and the contribution to the field. It should also reflect on the broader implications of the work.

7. **References**: Ensure that all references are up-to-date and relevant. Any old references should be replaced with the latest research where applicable.

8. **Data Availability**: The manuscript must adhere to our data availability policies. Please provide a clear statement regarding where the data supporting your findings can be accessed.

9. **Graphics Quality**: Some of the figures provided are not of high enough quality for publication. Please ensure that all figures are clear, high-resolution, and correctly annotated.

10. **Reviewers' Comments**: Please address all specific points raised by the reviewers in your revision. A detailed point-by-point response will be required to explain how you have addressed each comment or why a suggestion was not incorporated.

In conclusion, your manuscript has the potential to make a valuable contribution to our understanding of seabed topography. I invite you to revise your manuscript in line with the feedback provided and resubmit for further consideration. We look forward to receiving your revised manuscript.

Sincerely,

Md. Naimur Rahman

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. 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

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

Reviewer #1: No

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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

**********

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: 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: =================

General Comments:

=================

The present work aims to report on a comparative multi-site analysis of high-resolution topography surveys in rough nearshore environments, particularly those with rocky and coral seabeds. This analysis contributes to proposing a reduced set of relevant roughness estimators, with the aim of defining a unified framework for reconstructing roughness statistics and bathymetry from fine seabed topographical data.

For this purpose, the authors studied nine sites and quantified the geometrical structure of seabeds using various metrics. With this information, they attempted to identify representative estimators capable of quantitatively discriminating between seabed types.

The paper is well-organized, but some results need improvement, and certain issues require clarification. Some figures are of good quality, but others need improvement, as explained below in the specific comments.

Despite the need for some clarifications in the reviewer's opinion, this article should be interesting to the readership of PLOS ONE. The reviewer recommends the article for publication, with consideration given to the specific comments listed below.

==================

Specific Comments:

==================

The title appears too general, referring only to rough seabeds. I suggest the title should clarify whether the focus is specifically on rocky and coral seabeds.

L.180: The authors state, "The final selected profile 180 lengths are given in Table 1. T." In which column? This information is not provided there.

L. 299-300: The last sentence of the paragraph is poorly written. Please improve this.

L. 307-312: This analysis is poorly presented with incorrect values. The values mentioned in the paragraph do not correspond to those in Table 2, and it is unclear, based on the positive or negative values of kurtosis, why, for example, Maupiti A is considered a platykurtic distribution and Banneg a leptokurtic distribution. Please, carefully check this.

Figs. 10 and 11: The resolution of the PDF figures is poor, improving when opening the images in JPG. However, even with improved quality, the font size of letters and numbers is too small for correct reading. Please, improve it. Additionally, the caption of Figure 10 states, "The r displays the determination coefficient," but despite being difficult to discern, I believe what is being presented is the correlation coefficient.

L. 337-370: The values of the directionality index from Equation 11 are presented. However, when examining the respective initial figures (e.g., Fig.5), cross-shore and alongshore profiles appear to have been conducted with some obliquity to the coastline. The authors should discuss this because they make no mention of it and should also address the implications of this obliquity for the results.

L. 405: "they all describe" not "they all describes."

L. 434: The authors state, "the directionality index proposed by [51] from laboratory experiments, show good agreement with visual observations," but I believe no visual observations are presented before. Are these visualizations observable, i.e., can they be measured from images that corroborate the values of Equation 11? This should be clarified.

L. 525: Conclusion: The conclusions are presented in a very general manner. It is necessary to specify the conclusions reached by this work in relation to the objectives they set out to achieve. Please, rewrite this section more clearly.

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6. 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

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

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.

Revision 1

See attached documents

Attachments
Attachment
Submitted filename: AnsJournalRequirements.pdf
Decision Letter - Md. Naimur Rahman, Editor

PONE-D-23-30056R1Quantifying the topographical structure of rocky and coral seabedsPLOS ONE

Dear Dr. Sous,

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.

Please submit your revised manuscript by May 18 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,

Md. Naimur Rahman

Academic Editor

PLOS ONE

Journal Requirements:

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:

Please address all the comments from the reviewer carefully.

[Note: HTML markup is below. Please do not edit.]

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: (No Response)

**********

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: The answers and revisions to the paper seem to have been satisfactorily addressed. However, this verification cannot be viewed entirely because the revised paper has a problem with the figures.

In particular:

- The authors mention that they have introduced two additional new figures, totaling 15 figures. However, only 13 figures appear, as in the previous version of the paper;

- The figures appear in a disordered manner, and some are not always numbered, making direct analysis with the text difficult (13, 12, 9, 8, 7, 6, 5, 2, 1, ?, ?, 4 and 3!);

- Even the ones that are ordered do not correspond to the text's description. For example, at the beginning of the Results section, it mentions figure 8, but in the document, this seems to correspond to the figure indicated as number 7.

Therefore, the reviewer recommends correcting what has been described so that the article can be considered for publication.

**********

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

**********

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

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.

Revision 2

We are sorry for the inconvenience caused by the incorrect figure location which has been corrected in the new version of the paper.

Best regards

Attachments
Attachment
Submitted filename: AnsRev1.pdf
Decision Letter - Md. Naimur Rahman, Editor

Quantifying the topographical structure of rocky and coral seabeds

PONE-D-23-30056R2

Dear Dr. Sous,

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.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org.

If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

Kind regards,

Md. Naimur Rahman

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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: The answers and revisions to the paper are satisfactorily addressed and I consider that the paper is acceptable for publication.

**********

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

**********

Formally Accepted
Acceptance Letter - Md. Naimur Rahman, Editor

PONE-D-23-30056R2

PLOS ONE

Dear Dr. Sous,

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team.

At this stage, our production department will prepare your paper for publication. This includes ensuring the following:

* All references, tables, and figures are properly cited

* All relevant supporting information is included in the manuscript submission,

* There are no issues that prevent the paper from being properly typeset

If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps.

Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org.

If we can help with anything else, please email us at customercare@plos.org.

Thank you for submitting your work to PLOS ONE and supporting open access.

Kind regards,

PLOS ONE Editorial Office Staff

on behalf of

Mr Md. Naimur Rahman

Academic Editor

PLOS ONE

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