https://orcid.org/0000-0002-7703-0270
Peer Review History
| Original SubmissionAugust 25, 2020 |
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PONE-D-20-26698 Space-Time Surveillance of COVID-19 Emerging Hotspots using Prospective Scan Statistics Enhanced by Spatiotemporal Event Sequence Based Clustering PLOS ONE Dear Dr. Beard, 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 all the issues raised by the two reviewers Please submit your revised manuscript by Jan 29 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:
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, Agricola Odoi, BVM, MSc, PhD, FAHA, FACE Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and 2. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. 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We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text: “I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.” 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].” 4.2. 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/ [Note: HTML markup is below. Please do not edit.] 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: Partly Reviewer #2: Partly ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ********** 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 ********** 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 ********** 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: The authors of the study used prospective space-time scan statistic on number of positive COVID-19 cases in counties to determine location and period of most likely space-time clusters in the continental US. Case counts from counties in most likely clusters were then analyzed through hierarchical agglomerative clustering method to further characterize groups of counties with similar patterns in how frequency of cases (standardized by population size) develop over time. Demographic factors were then used in order to evaluate any differences between clusters. Researches reported that counties detected in the same space-time clusters were classified into different hierarchical clusters. This is interesting finding, and a topic worthy of investigation; although not completely surprising. When methods are combined, this could be done in many different ways and authors used one possible approach - at the very end of the manuscript, they offered some alternatives. This alternative approach was something that I was wondering from the very beginning (no actionable comment here). In my opinion, by far the largest limitation of the manuscript is its length. Manuscript with 38 pages of text (including tables) is more a technical report than a classical journal article. This is clearly a consequence of thorough analysis, but reading of such contribution is very demanding on the reader, particularly when a lot of technical results consists of reporting counties in most likely clusters. This was done for different time periods, followed by hierarchical clustering. Of course, number of clusters in spatial analysis and in multivariate analysis will be different and this further complicates reading. Is it possible to present an analysis for only one time period (the one authors feel is the most informative), and for the rest of results to be offered in the supplementary material? With a short commentary point on how are other results similar or dissimilar? Also, in multivariate cluster analysis, it is often attempted to explain nature of clusters identified. Although this was attempted to some degree here, this information was diluted among many other details. Because of manuscript length, it is easy to miss some technical details. For example. L104 - are the authors suggesting that RR is available for each location in the cluster? I am not sure that this is in line with how scan statistics work. The RR risk is estimated for the population in the scanning window, or maybe I missed the point here. L116. Is it possible to determine false positives based on results from scan statistics? Could RR<1 be indication of cluster of cases with lower than expected risk, rather than false positive? L121. Perhaps check wording. Is it all counties with high RR or all counties from significant clusters with high RR? L159. Is "severe" the best adjective to use. severe typically refers to clinical expression, whereas cases are just reflection of incidence, some are likely asymptomatic. L163. Authors should perhaps explain whether they used Poisson model or space-time permutation model. They are different methods. L163. In this section, it would also be useful to explain how is prospective statistic different from retrospective which is commonly applied in retrospective research studies. In the methods section - authors did not mention division into different time periods, and what was the rationale for that. reader learns about that in the results section. L239. "spread" may not be the best word to use here. Clusters do not spread. Throughout the manuscript, some wording should be improved. e.g. L384 writes about 4 statistically significant counties. is it counties or clusters that are significant? In addition, the authors try to compare demographics across different clusters, but are not trying to do any statistical testing which could be helpful as a decision point. Is there a reason for that? Are the authors concerned that many comparisons could lead to some false findings? Reviewer #2: Manuscript #: PONE-D-20-26698 Title: Space-time surveillance of COVID-19 emerging hotspots using prospective scan statistics enhanced by spatiotemporal event sequence based clustering. Authors: Fuyu Xu & Kate Beard General comments: Xu and Beard have used an innovative approach to classifying the temporal patterns of “epidemic curves” at the county level that could make a very important contribution to the epidemiological and disease surveillance literature. Unfortunately, the current manuscript suffers from too much repetition, taking on too many objectives, and perhaps taking a less than ideal approach for integrating their event sequence based clustering with scan statistics. Specifically, the following should be addressed: 1. While there are a number of good reasons to conduct prospective scans, in the context of this manuscript repeating the analysis several times for different periods during the pandemic in the contiguous US states makes the manuscript exceedingly repetitive. I would recommend the authors pick a single period for the analysis and use it consistently throughout the manuscript to exemplify their approach. 2. In terms of the use of the scan statistic, there are a number of major issues that should be addressed by the authors: i. The decision to limit the maximum size of a cluster to 10% of the population appears to be arbitrary. I would recommend using the default of 50% or less (also the maximum that can be used) of the population. This value does not prevent smaller clusters from being detected, but prevents the need for arbitrary values and is the whole point of the flexible scanning window. In reviewing the figures, it is clear that during certain periods a large number of small clusters are likely part of a larger cluster. ii. The authors need to clearly state what rule was used for reporting space-time clusters in terms of spatial overlap and preferably spatio-temporal overlap. iii. The authors are unclear whether they are using a Poisson model or the space-time permutation model for their space-time scans. On lines 166-167, they refer to the permutation model and later to the Poisson distribution on line 185. The space-time permutation model is not based on a Poisson distribution and only requires case data. iv. If the authors used a Poisson model in SaTScan, it is unclear why they did not adjust for age and sex; this type of standardization is common in most epidemiological analyses. If they used a space-time permutation model, they should recognize that these models identify space-time clusters while inherently adjusting for purely spatial and temporal clusters; in other words this model would adjust for demographic and socio-economic factors if they were related to spatial location. 3. It is unclear why the authors did not apply their event sequence based clustering to all counties. The value seems to be diminished by only applying the technique to locations within active space-time clusters. In fact, investigating if there were spatial clusters of these event sequence clusters, using a multinomial model, would have been a very interesting and perhaps a more appropriate way to combine the two approaches and comment on whether or not these event sequence clusters were randomly distributed or had particular “hotspots”. It would certainly be interesting to compare space-time “hotspots” for rates of disease with spatial clusters of these event sequence clusters. 4. The event sequence clusters shared in geographically distant regions (e.g., Pacific Northwest and New York) likely reflect when COVID-19 was introduced into the US even though molecular sequencing suggests the introduction in these regions was likely from different continents of origin (i.e., Europe vs. Asia). Some discussion concerning the epidemiological interpretation of clusters based on the greater literature is warranted. 5. The socio-demographic analyses should probably be removed from this manuscript. I would recommend performing these analyses using multivariable multinomial regression models based on the event sequence cluster classification for each county in a separate manuscript. Currently, the descriptive comments concerning socio-demographic factors within clusters identified using different methods are not particularly insightful in the current draft of the manuscript. I suspect the authors have put too much in one manuscript and this section deserves much more detail and a stronger analysis. Specific comments: Title: i. The event sequence based clustering was applied to counties during a specific time period, but it did not account for spatial location. It might be better for the authors to state that they are examining the distribution of counties classified based on event sequence based clustering with respect to space-time clusters of COVID-19. If they agree with comment 3 in my general comments, it might be better to focus on the spatial clustering of event sequence based clusters of COVID-19. Introduction: i. Lines 60-62: This statement is not really correct. Where and when these measures were implemented, there was success in “flattening the curve” (even in the US), and strict measures did control the disease in parts of the world where the political, economic, and sociological conditions allowed for their strict implementation. I would remove this sentence since it is not relevant to the authors’ work or the need for surveillance tools for the continuing pandemic. ii. Lines 97-98. This statement is not accurate. The space-time permutation model that is available with SaTScan does not use or require background population data although as a result, it is subject to population shift bias. iii. Lines 108-109. There’s nothing that prevents an individual from making these comparisons. Please note that the point of the scan statistic is to detect if there are clusters in space, time, and space-time with significantly higher or lower levels of disease without predefining the geographical or temporal size of these clusters. There is no implication that every sub-region within a cluster shares the same rates any more than one could assume that the rate of disease among cities, towns, or villages within a county were homogeneous. iv. Lines 110-129. This reads more like a summary of methods. I would strongly suggest the authors clearly state their research objectives (i.e., what are they trying to discover or compare rather than a brief description of the methods). Methods: i. Please review suggestions in the general comments especially concerning the scan statistic. ii. Lines 156-161. The authors should use appropriate epidemiological terms. The authors need to clearly state they are calculating the crude incidence rate. However, I would strongly encourage them to consider calculating the age and sex adjusted incidence rates for their subsequent event sequence based clustering. iii. Lines 183-184. The authors state that the duration of a cluster was set at 2 days, but in the results they have space-time clusters of 1 day in length. The authors should revise the methods or results for consistency. iv. Line 188. Please note the number of Monte Carlo replications performed and whether scans were performed as 1-tailed tests needs to be stated. v. Line 198. Please replace the phrase “cases normalized to the county population” with the term incidence rate throughout the manuscript. Results: i. Please make certain tables of clusters have consistent titles and select one short form to differentiate event sequence based clusters from space-time clusters and use it consistently throughout the manuscript. Please avoid repeating the methods in the results and use subheadings to differentiate the different statistical approaches being used. Avoid including discussion in the results section. ii. The tables and figures provide a great deal of summary detail. Please use the text to describe general locations and major characteristics of clusters. The listing of each county within a cluster or each county with a high rate of disease in the text is not necessary. For tables of space-time clusters, please include a column for the radius, the column for the log likelihood in unnecessary. Some authors would include latitude and longitude in these tables, but the figures are sufficient for spatial information. iii. The figures concerning the “elbow method” and the dendrograms should be moved from the supplemental material into the main manuscript. If the authors follow the suggestions in the general comments, this figure would only be needed for the one period being examined. iv. Line 339. Please remove the term “emerging”. v. Line 450. Please note that it is the cluster that is statistically significant and not the counties. Please remove similar phrases from the text. vi. Line 473. Figures and tables need to be numbered in the order they appear in the text. Currently, figure 9 is listed before figures 7 and 8. vii. Line 522-523. Please remove results that are not statistically significant from the text and figures. Discussion: i. Please revise the discussion after revising the manuscript. References: i. Please make certain the references are consistently formatted and all information is included. For instance, the formatting of journal titles in terms of capital letter is inconsistent and the journal is missing from some references. Tables and figures i. Please do not include Excel files in the supplemental material. If you believe this material is useful for the reader, generate tables in PDF format with proper variable names and footnotes for any short forms. ********** 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 Reviewer #2: 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 |
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PONE-D-20-26698R1 A comparison of prospective space-time scan statistics and event sequence similarity-based clustering for COVID 19 surveillance PLOS ONE Dear Dr. Beard, 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 all the issues raised by both reviewers. Please submit your revised manuscript by May 02 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:
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, Agricola Odoi, BVM, MSc, PhD, FAHA, FACE 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. [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: All comments have been addressed Reviewer #2: (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 Reviewer #2: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 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: Thank you to authors for addressing points raised in the previous review. I only have a couple of minor suggestions for authors to consider. Authors stated that incubation is 14 days, which is approaching upper limit. Ideally, the authors should carefully word whether this was maximum or average and provide reference. Next, on images displaying case sequence clusters – it may be useful to indicate, possibly in the figure legend, what are outsiders. Similarly, for cluster dendrograms it may be helpful to indicate which group of observations belong to which cluster. It seems there is a place for this, but cluster designation is not visible on figures. In addition, the authors used calendar time to look into similarity of case incidence within clusters. For future consideration, it may actually be interesting to consider time in terms of number of days since detection of the first case in a county. Reviewer #2: Manuscript ID: PONE-D-20-266698R1 Title: A comparison of prospective space-time scan statistics and event sequence similarity-based clustering of COVID-19 surveillance Authors: Xu, F. & Beard, K. General comments: The revised draft of the authors manuscript is greatly improved. Although I am not sure I agree with all their decisions (e.g., maximum scanning window), I believe they have documented/defended their decisions well. My remaining suggestions are mainly cosmetic in nature. Below are some general comments/suggestions: i. Please put subheadings for the space-time cluster and sequence similarity-based cluster paragraphs in each study period section to avoid confusion over what type of “clusters” are being discussed. ii. Spell “sequence similarity-based cluster” consistently throughout the manuscript. It is written at least three different ways in the text (e.g., “sequence-similarity based cluster”, “sequence similarity based cluster”). iii. In paragraphs concerning sequence similarity-based clusters, please do not refer to “spatial clusters” of these clusters. It is very confusing to use the term in a non-statistical sense in a manuscript describing two types of statistical clusters. Just indicate that these sequence similarity-based clusters concentrate around particular cities or regions rather than state they form “spatial clusters”. iv. In the discussion, make certain to state clearly the value of extracting the information concerning the sequence similarity-based clusters from within the space-time clusters. Manuscript text: i. Line 45: It should read “share a similar”. ii. Line 109: It should read “understanding disease dynamics”. iii. Lines 113 & 386: It should read “complementary” not “complimentary”. iv. Line 165: It might be better to write “missing” rather than “avoiding”. v. Lines 171-173: This statement is not accurate. The age structure of a population will influence disease reporting and the real incidence of disease. The authors should just state they did not have access to age and sex data for cases and were unable to adjust for these variables as they reported in their response letter. This limitation should be addressed in the discussion. vi. Line 219: Would it be better to state “decreased” rather than “improved”? vii. Line 263: It should read, “statistical”. viii. Line 333: Please remove the sentence, “In this period, we note little activity on the west coast.” This statement is not correct. The authors did not identify any active space-time clusters during this period, but there was a lot of disease activity on the West Coast. ix. Line 347: Replace “covering through” with “ending in”. x. Line 348: Replace “statistics” with “statistic”. xi. Line 362: Replace “determined” with “selected”. xii. Lines 371-372: Make certain to explain what “OC” means in the text. xiii. Lines 389-390: It might be better to state, “the expected number of cases in space-time based on …...”. The following sentence from 390-391 should be removed since it is redundant with the addition of the above phrase. xiv. Line 392: It should read, “at such a location during a period of time.” xv. Line 393: Replace “temporal dimension” with “temporal pattern” since one could argue the “temporal dimension” is part of the space-time cluster. xvi. Line 400: Rephrase as “we found that in all study periods, similar sequence patterns of COVID-19...” xvii. Line 408: Consider including “similar changes in surveillance programs” to the list of reasons explaining these common temporal patterns. xviii. Lines 413-414: Do the authors mean “counties in New York State”? Please clarify. xix. Line 447: It should read, “pathway studies”. Tables and figures: i. Tables 1-4. In the titles, please replace “SaTScan space-time clusters” with “prospective space-time clusters”. A footnote can be added to the tables stating, “Space-time clusters were identified using the spatial scan statistic with a Poisson model”. ii. Fig 1. Remove “covering” from the title. iii. I believe the journal expects supplementary materials to be labeled as “Table S1” and “Fig. S1” rather than “S1 Table” or “S1 Figure”. Please correct accordingly. References: i. Please properly edit the references. Journal titles and manuscript titles are inconsistently formatted. Additional “PubMed” information is sometimes accidentally included at the end of references. If the authors wish to include “doi” information, please include it consistently or not at all. ii. Reference 36 should be replaced with a more formal reference (e.g., journal article or government report). ********** 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 Reviewer #2: 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 |
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PONE-D-20-26698R2 A comparison of prospective space-time scan statistics and spatiotemporal event sequence similarity-based clustering for COVID 19 surveillance PLOS ONE Dear Dr. Beard, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit and will most likely be accepted after the minor revisions suggested by reviewer 2 have been implemented. Therefore, we invite you to submit a revised version of the manuscript after making the recommended revisions. Please submit your revised manuscript by Jul 02 2021 11:59PM. 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:
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. 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, Agricola Odoi, BVM, MSc, PhD, FAHA, FACE 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. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. 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Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. 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 #2: Manuscript ID: PONE-D-20-26698R2 Manuscript title: A comparison of prospective space-time scan-statistics and spatiotemporal event sequence-based clustering for COVID 19 surveillance Corresponding author: Beard-K General comments: The authors have made all the requested revisions. Below are some minor edits/suggestions they should consider. There is no need for me to see the manuscript again. Specific comments: Line 172: Should it read, “required”? Line 174-175: It might sound better to write, “....for cases in this study, so we could not adjust for age and sex.” References: Fix the formatting of journal titles for references 17, 21, 34 (also the article title). ********** 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 [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 3 |
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A comparison of prospective space-time scan statistics and spatiotemporal event sequence similarity-based clustering for COVID 19 surveillance PONE-D-20-26698R3 Dear Dr. Beard, 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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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, Agricola Odoi, BVM, MSc, PhD, FAHA, FACE Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-20-26698R3 A comparison of Prospective Space-time Scan Statistics and Spatiotemporal Event Sequence Based Clustering for COVID-19 Surveillance Dear Dr. Beard: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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 Prof. Agricola Odoi Academic Editor PLOS ONE |
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