PONE-D-21-35676

FRAME - Monte Carlo model for evaluation of the stable isotope mixing and fractionation

PLOS ONE

Dear Dr. Lewicki,

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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

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: General comments

This paper describes a computational model for unraveling mixing and isotopic fractionation that occurs various environmental/geochemical/ecological settings. Since stable isotope ratios often show distinct values between different source materials, isotope ratios of a sample and its potential sources are compared to estimate contribution from each source. However, it is not always the case that proportions of the sources are algebraically calculated because of too many potential sources or isotopic change (fractionation) during chemical/physical conversion of target compounds after mixing. In addition, error associated with the source partitioning is not easy to derive. The authors developed a convenient and flexible tool that can calculate mixing rate of sources with probability distributions and effect of other factors such as isotopic fractionation. They also present many examples showing how the tool can resolve the mixing problems of real conditions appropriately.

Although I cannot fully evaluate the mathematical theory part because it is outside my area of expertise, I think this paper will bring great benefits to researchers using stable isotopes to elucidate material cycles in a variety of disciplines. I recommend its publication after addressing following points.

Specific comments

Abstract. The authors write “this tool can also be useful for non-stable isotope studies”, but no example of such application is listed. It would be better to add some ideas.

L17–18. I think there was an attempt at estimation of errors in source partitioning with consideration of isotopic fractionation although the approach was simpler than the present study (Toyoda, S., Yano, M., Nishimura, S., Akiyama, H., Hayakawa, A., Koba, K., et al. (2011). Characterization and production and consumption processes of N2O emitted from temperate agricultural soils determined via isotopomer ratio analysis. Global Biogeochem. Cycles, 25, GB2008).

L33–43. In the work of Lewicka-Szczebak et al. (2020) they compared two cases: 1) N2O reduction by denitrification first occurs and then mixed with N2O from other sources, 2) N2O reduction occurs after mixing. But in the present paper, it seems only the case 2) is considered. Can the developed tool also simulate the case 1)?

L129. Correct typo (1,m]

L422–425. Although it is not critical in the context, it would be better to note that overall isotope fractionation is not always equal to simple sum of fractionation for the two step in order to avoid misunderstanding.

Figure 1 caption, the last line, “The bottom right panel”. LEFT panel? Also please add titles of axes, same for other figures.

Figure 2. Some characters in the figure do not correspond to those explained in the caption. I think the axis titles “X” and “Y” must be “I1” and “I2”, respectively. Also “M” means x?

Figure 3. I cannot understand why one can tell “the stabilization is achieved” from the figure. To my eyes, oscillating feature is almost the same between before and after the dashed line.

Figures 16–19. It is confusing that caption says the authors consider only three endmembers while five sources are plotted in the figure.

Reviewer #2: The paper presents a working open source framework for stable isotope analisys.

The software is user friendly and shows some original features in respect to other similar works. In particular it can consider fractination process besides isotope mixing.

The paper is quite well written and clear. There are just some minor notes and suggestions for authors:

- The examples are usually well presented and references are always given. However, there can be some difficulties for readers to get a rapid introduction to them. A small introductiion paragraph for each example, what is the addressed problem and what can be gained with isotope analisys, can increase readability.

- The software works flawlessly on Linux/wine, however it is not well clear what is the right combination of data/source/model for each example. Here also an introduction would be welcome. A comment part in the data file would be very useful.

- In the last paragraph of the comment of Figure 1, I think there is an error: right --> left.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-21-35676R1FRAME - Monte Carlo model for evaluation of the stable isotope mixing and fractionationPLOS ONE

Dear Dr. Lewicki,

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 Dec 01 2022 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 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,

Viacheslav Kovtun, Dr.Sc., Ph.D.

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.

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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: (No Response)

Reviewer #2: All comments have been addressed

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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

Reviewer #2: Yes

**********

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

Reviewer #1: N/A

Reviewer #2: N/A

**********

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

Reviewer #2: 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

Reviewer #2: Yes

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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: In the revised manuscript, the problems I pointed out have been improved. I think it is now acceptable after a few minor corrections below.

L12–13. I cannot understand why the authors revised this phrasing while they did not change the words at L4. I cannot make sense out of the phrase "n elements stable isotope composition determination"

L50. Typo. “signature”

Reviewer #2: (No Response)

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Reviewer #2: No

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FRAME - Monte Carlo model for evaluation of the stable isotope mixing and fractionation

PONE-D-21-35676R2

Dear Dr. Lewicki,

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,

Viacheslav Kovtun, Dr.Sc., Ph.D.

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

Reviewer #2: 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

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: N/A

**********

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

Reviewer #2: 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

Reviewer #2: 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: (No Response)

Reviewer #2: All comments have been addressed.

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Reviewer #1: No

Reviewer #2: No

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