Bayesian inference of COVID-19 spreading rates in South Africa

Rendani Mbuvha; Tshilidzi Marwala

doi:10.1371/journal.pone.0237126

Peer Review History

Original SubmissionApril 28, 2020
11 Jun 2020 Decision Letter - Jeffrey Shaman, Editor PONE-D-20-12397 Bayesian Inference of COVID-19 Spreading Rates in South Africa PLOS ONE Dear Dr. Mbuvha, 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 respond to the reviewer comments on a point-by-point basis and revise the manuscript accordingly. Please submit your revised manuscript by Jul 26 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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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, Jeffrey Shaman 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2.We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: - arXiv:1906.06382v1 -https://www.medrxiv.org/content/10.1101/2020.04.07.20057133v2 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. Please also ensure you have described the source of your data in the methods section, including a link or citation which can be used to access the data. 3. Please ensure that you refer to Figures 10,11 & 12 in your text as, if accepted, production will need this reference to link the reader to the figure. 4. Please upload a copy of Supporting Information Appendix S1 which you refer to in your text on page 11. [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: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: In their paper the authors analyse with Bayesian methods the increase of COVID-19 case numbers in South Africa. They find two change points in the propagation that they link to respectively to travel bans/containment of infections and onset of massive testing. They conclude that the governmental interventions linked to the first change point were effective. I recommend this paper for publication because of its timeliness and well described methods and would suggest a few minor revisions: - In table 2 the authors list compare different sampling methods by their LOO statistic. As far as I understand it this is not useful and misleading. The LOO statistic was developed to compare different models (which are also correctly shown in this table). The lower LOO statistic of the MH sampling probably arises from a incomplete sampling of the posterior which could potentially be fixed letting the chains run longer and/or with a longer burn-in period. A useful statistic to check convergence is the Rhat statistic (https://docs.pymc.io/api/stats.html#pymc3.stats.rhat). - The scale of the lambda_2 prior in the table 1 doesn't seem to match the prior distribution plotted in Fig. 4. The authors could also think about whether the lambda 1 and 2 priors are well motivated, and eventually make them wider/more uninformative. The posterior of the Lambda 1 prior is in the tail of the prior distribution (Fig. 4). - In the algorithm of the HMC, in the third line of the leapfrog loop, the closing bracket after "p(t" should be removed. ****** 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: Yes: Jonas Dehning [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. https://doi.org/10.1371/journal.pone.0237126.r001
Revision 1
7 Jul 2020 Author Response Dear Editor Kindly find our responses to reviews below. Best, Rendani Mbuvha ----------------------------------------------------------------------------------------------------------- Responses to Academic Editor 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 https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Response We have made changes in line with the formatting guidelines, including: Changing the affiliation of one author from 'office of the vice-chancellor(his office)' to the institute that he is affiliated to at the university Changing 'figure' references to 'fig' Moving supporting information to an appropriately named appendix Changing subsection headings accordingly 2.We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed: - arXiv:1906.06382v1 -https://www.medrxiv.org/content/10.1101/2020.04.07.20057133v2 In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed. Response: We have made changes in terms of rewriting, rephrasing(with referencing) and inserting quotations in areas where there was previous overlapping text with our earlier preprints outside the methods section. Please see highlighted changes. Please also ensure you have described the source of your data in the methods section, including a link or citation which can be used to access the data. Response: We have added a description of our data source, including the necessary citation. 3. Please ensure that you refer to Figures 10,11 & 12 in your text as, if accepted, production will need this reference to link the reader to the figure. Response: These figures have now been moved to the supporting information files with the relevant references included in the main text. 4. Please upload a copy of Supporting Information Appendix S1 which you refer to in your text on page 11. Response: Now included as separate files - ( this mainly consists of the previous ‘figures’ 10-12 and other diagnostic plots) --------------------------------------------------------------------------------------------------------------------------------- Responses to Reviewer 1 I recommend this paper for publication because of its timeliness and well described methods and would suggest a few minor revisions: - In table 2 the authors list compare different sampling methods by their LOO statistic. As far as I understand it this is not useful and misleading. The LOO statistic was developed to compare different models (which are also correctly shown in this table). The lower LOO statistic of the MH sampling probably arises from a incomplete sampling of the posterior which could potentially be fixed letting the chains run longer and/or with a longer burn-in period. A useful statistic to check convergence is the Rhat statistic (https://docs.pymc.io/api/stats.html#pymc3.stats.rhat). Response: We agree with the reviewer. We have revised table 2 to only refer to the comparison between models rather than include samplers. We have also increased the number of chain runs to 5000 and increased burn-in to 1000 runs with ten concurrent chains rather than four to increase the likelihood of convergence. - The scale of the lambda_2 prior in the table 1 doesn't seem to match the prior distribution plotted in Fig. 4. The authors could also think about whether the lambda 1 and 2 priors are well motivated, and eventually make them wider/more uninformative. The posterior of the Lambda 1 prior is in the tail of the prior distribution (Fig. 4). Response: We have now changed both priors for lambda 1 and lambda 2 to a wider and relatively less informative LogNormal(log(0.4),0.7). The change in priors and running the chains for longer marginally changes mean estimates of posterior parameters -- this does not seem to change the overall findings in a material way. - In the algorithm of the HMC, in the third line of the leapfrog loop, the closing bracket after "p(t" should be removed. Response: We have amended the formula typo accordingly. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0237126.r002
22 Jul 2020 Decision Letter - Jeffrey Shaman, Editor Bayesian Inference of COVID-19 Spreading Rates in South Africa PONE-D-20-12397R1 Dear Dr. Mbuvha, 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, Jeffrey Shaman 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 concerns have been fully addressed and in my opinion the manuscript is now 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: Yes:** Jonas Dehning https://doi.org/10.1371/journal.pone.0237126.r003

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