PONE-D-19-17270

Plant mediated community structure of spring-fed, coastal rivers

PLOS ONE

Dear Dr. Lauretta,

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As noted above, I am asking that you prepare and submit a revised version of your manuscript. I characterized the requested revision as a major rather than minor revision because one of the recommended changes requires you to recalculate your measures of prediction error or model fit for scenarios 1 through 4.

In preparing your revision, please respond to each issue raised by Reviewer 1 and myself in our reviews. Most of these are minor issues that merely require clarification or rephrasing of various parts of the text. Three more-substantive issues I wish to highlight are the following:

1. As I explain in my review, I think it is important that you modify your measure of prediction error (or goodness of fit) to make it dimensionless, since terms in the current X^2 formula do not share the same physical dimensions and therefore should not be added. I suggest a simple alternative in my review. This change requires recalculation of the values listed in Table 6, but I will be surprised if it changes your conclusions.

2. Please clarify in the text that you are not performing statistical model selection or statistical goodness-of-fit assessments, and therefore no formal tests of statistical significance are performed. Both Reviewer 1 and I were initially puzzled by the way you currently describe your measure of goodness of fit. By calling it "chi-squared" and stating in the abstract that you perform "goodness-of-fit tests", you suggest to readers that you are performing chi-squared tests of statistical significance, but you actually do not do that.

3. Please be sure to address the question by Reviewer 1 regarding availability of all data from your study.

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James N. McNair, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

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Comments to the Author

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

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Reviewer #1: Partly

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

Reviewer #1: Yes

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Reviewer #1: No

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Reviewer #1: Yes

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5. Review Comments to the Author

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Reviewer #1: The manuscript appeared to be technically sound with the overall conclusions supported by the modeling results. Nevertheless, I did have two questions regarding the interpretation of results. (a) Is it problematic that none of the models seem to be similar to the Chassahowitka River? Why were the results of Model 1 not more similar to the Chassahowitka River (see Fig. 6)? (b) From a philosophical perspective, what if all the models you tested were "bad"? How would those results differ from what was found? The approach seems to evaluate which is the best model among the ones tested, but how do we know if any of the models are "good"?

The Ecopath/Ecosim modeling seemed appropriate as well as the approach used to evaluate competing models. I initially expected AIC to be used to evaluate models, but it is not straightforward to me how such an approach could be implemented given the structure of the models being evaluated. Some clarifications are warranted, especially for readers that do not have a deep understand of Ecopath/Ecosim. (a) P/B and Q/B ratios should be clearly defined in Table 2. Make sure Walters et al. (2008), which is cited in Table 2, is listed in the references. (b) Provide more context for interpreting the Chi-squared statistics reported in Table 6. What do small and large values indicate? What is the null hypothesis underlying the Chi-squared statistic? Is there a way to calculate p-values for the total Chi-squared statistics? How common is this type of approach (i.e., using Chi-squared statistics) for evaluating these types of models? (c) Can you provide context for why a bootstrapping procedure was used for estimating mean trophic group biomass (Lines 167-168)?

The data from the modeling output do not seem to be fully available. If this is the case, then this should be easily addressed by providing the output in supporting information.

Overall, the manuscript was well written and easy to follow. The quality of Figures 4, 6, and 7 made interpretation difficult, but this was likely the result of the file I printed.

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Reviewer #1: No

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Plant-mediated community structure of spring-fed, coastal rivers

PONE-D-19-17270R1

Dear Dr. Lauretta,

I am pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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Thank you for submitting your work to PLOS ONE.

With kind regards,

James N. McNair, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

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