PONE-D-20-15142

DDRP: real-time phenology and climatic suitability modeling of invasive insects

PLOS ONE

Dear Dr. Barker,

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.

The reviewers and I agree that this a well-written manuscript. I appreciate your attention to detail and your thorough explanations of the choices you made in developing DDRP. However, Reviewer 1 expressed reservations about the lack of underlying hypotheses and validation, and I share some of those concerns. As you are probably aware, PLOS ONE has a specific set of criteria for manuscripts that present new software. These criteria relate to utility, validation, and availability (https://journals.plos.org/plosone/s/submission-guidelines#loc-methods-software-databases-and-tools). With respect to validation, “the submitted manuscript must demonstrate that the new tool is an improvement over existing options in some way. This requirement may be met by including a proof-of-principle experiment or analysis; if this is not possible, a discussion of the possible applications and some preliminary analysis may be sufficient.” I believe your goal is to see wide uptake of DDRP, which means that you must meet a fairly high standard for validation that goes beyond preliminary analysis. Certainly, your discussion of the practical advantages of DDRP over alternatives is compelling, but it would be much better if you provided quantitative evidence.

I encourage you to look to the comments of Reviewer 1 for potential opportunities to evaluate model performance. For instance, it should be relatively straightforward to implement (holdout) validation of the predicted distributions for your two example cases and derive some estimates of the error rates. Additionally, you should be able to devise some sort of test of the relative merit of your degree-day modeling method, even with limited data.

Please submit your revised manuscript by Aug 31 2020 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.

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We look forward to receiving your revised manuscript.

Kind regards,

Frank H. Koch, PhD

Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

Minor comments:

Table 1 – references/citations for these parameter values? (I realize they’re provided later but it would be good to include references in the caption for readers)

Line 215 – delete “estimates of” (redundant)

Line 271- “high” instead of “highly”

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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: No

Reviewer #2: Yes

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

Reviewer #1: No

Reviewer #2: N/A

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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: Yes

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: Barker et al. provide a well written accounting of DDRP, a new software package to calculate degree days and climatic suitability for insects. The authors are correct that refinements are needed to prepare forecasts of the potential distribution and activity of insects over time. Such forecasts could be useful to refine surveys, particularly for invasive species whose complete current distribution may not be known with confidence.

While I do not find any errors, per se, I do not find any underlying hypotheses to underpin the research. One set of hypotheses could be related to the ability of the model to reproduce the distribution or activity of the light brown apple moth or the small tomato borer, the example cases that were provided. Ideally, these forecasts would be for areas that were not used for model development. Such validation is routine for these types of models and is a bare minimum. The model might have high commission error rates, classifying more areas as suitable than exist. It is not clear how well the model performs with respect to seasonal activity/phenology.

The authors discuss at great length different methods of estimating degree days. An argument is made that the method of calculation could result in quantitatively and qualitatively different forecasts. Such a suggestion is intriguing (and is certainly the subject of several other research papers), but the authors provide no new evidence (e.g., trap catch data over time) to demonstrate that the method they selected was substantially better, worse, or no different from other methods.

Another set of hypotheses could be related to the marginal improvement in model forecasts over existing models. As the authors correctly note, a number of platforms exist to provide national degree days based on recent weather. (I was a bit surprised to not see any mention of the Spatial Analytic Framework for Advance Risk Information System [SAFARIS] also sponsored by USDA APHIS.) The authors suggest that one distinguishing feature of the current model is the ability to account for variation in response to degree day accumulations. Yet, no data are provided to measure how the forecast is improved when such variability is added.

The authors description of the method of calculating cold and heat stress is vague. Do they use the same fundamental formulas as are used in CLIMEX. Why? Have they independently vetted those indices to determine how well they perform? Further, why do stress indices need to be determined on a daily basis? Again, with no formal comparisons, I am unclear what new insights the model is providing over existing models.

This model was developed with support from the Cooperative Agricultural Pest Survey. Can the authors describe how surveys were conducted before the development of this platform? How have they changed in response? Is there any evidence that trapping is now more efficient?

Current conclusions are not based on the results of the study. They are primarily aspirational.

Reviewer #2: This article describes a new a new multi-species spatial modeling platform that integrates mapping of phenology and climatic suitability in real-time which has applications for invasive pest detection and management. While many insect phenology modeling platforms are currently available, none to my knowledge, consider that multiple insects cohorts emerging at different times.

Overall, the manuscript is well written. The authors provide good justification for their modeling parameters and adequately discuss the limitations of DDRP. The authors develop two solid insect pest model examples in DDRP which highlight the platform’s products and potential as a decision support tool. The modeling is sound, and the R code is readily available online. There is very little that I can fault here. This article is certainly suitable for publication in Plos One.

General Comments:

The manuscript is a bit on the long side. I would recommend some trimming in the discussion section.

Line by Line comments:

143: Replace “ have simulated” with “simulate”

171: Replace “develop” with “development”

226: Replace “is” with “in”

400-405: DDRP seems like it would have a steep learning curve given that it runs best on a Linux OS and requires knowledge of R. How are these forecasting maps going to made available to pest managers and growers planning their pest management schedule for the growing season?

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Reviewer #1: No

Reviewer #2: No

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PONE-D-20-15142R1

DDRP: real-time phenology and climatic suitability modeling of invasive insects

PLOS ONE

Dear Dr. Barker,

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.

From the Academic Editor: Thank you for working to address the concerns raised during the first round of reviews. In particular, I believe your manuscript is stronger now that it includes and reports on some validation procedures. Reviewer #3 (added for the second review round) provided a handful of relatively minor comments and suggestions. If you address these, the manuscript should be suitable for publication.

Please submit your revised manuscript by Jan 10 2021 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: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Frank H. Koch, PhD

Academic Editor

PLOS ONE

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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 #2: All comments have been addressed

Reviewer #3: (No Response)

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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 #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #2: (No Response)

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: Yes

Reviewer #3: 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 #2: (No Response)

Reviewer #3: Overall

This is a very thorough, clear description of a new approach for modeling both species phenology and climate suitability for insect pests. I have only a handful of suggestions for improvements.

Specific things

Abstract

- L3 – “multi-species” is a bit confusing here – prior to reading the whole paper, it’s unclear whether this means that the system can handle multiple species at once (+interactions among them?) or rather that the system is species-agnostic

- L12 – “products” – maybe “outputs” works better here?

- L14-15 – the CLIMEX models bit here is hard for a reader unfamiliar with this to grasp in an Abstract (without the more complete description and explanation provided in the text). Maybe this sentence could be something like “Inputted species parameter values can be derived from laboratory or field studies or established through an additional modeling step.”

Main text

- L200 – “stadium” – is this a typo? Just checking – I don’t have an entomology background

- L440 – this mention of uspest.org seems out of the blue. USPEST is mentioned once early in the paper (L55), though it’s not made clear that the authors run this program or how it intersects with the DDRP package described in this manuscript.

- L457-459 – what is the source of these data? How were they collected? Just a few brief, key details would suffice and be helpful here

- L539 – why did you force Fahrenheit to integer values?

- L856 – “depository” (twice) – maybe “repository” works better?

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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 #2: No

Reviewer #3: 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.

DDRP: real-time phenology and climatic suitability modeling of invasive insects

PONE-D-20-15142R2

Dear Dr. Barker,

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.

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Kind regards,

Frank H. Koch, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Thank you for completing a final set of revisions. I appreciate your efforts to address all reviewer comments in this and the previous rounds of review.

Reviewers' comments: