COWAVE: A labelled COVID-19 wave dataset for building predictive models

Melpakkam Pradeep; Karthik Raman

doi:10.1371/journal.pone.0284076

Peer Review History

Original SubmissionOctober 6, 2022
12 Dec 2022 Decision Letter - Hilal Tayara, Editor PONE-D-22-27577COWAVE: A Labelled COVID-19 Wave Dataset for BuildingPredictive ModelsPLOS ONE Dear Dr. Raman, 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 Jan 26 2023 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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Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ****** 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: No ****** 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 ****** 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 manuscript is interesting; however, the following comment should be addressed: 1: All the sections and subsections must be included in the text, Such as :( Data and Methods, Smoothing Algorithms, etc.). 2: The abstract needs to be improved to do justice to the main contributions of the paper, also it contains some abbreviations that need to be explained. 3: The contribution is not stated also add it at the end of the introduction section. 4: Please add future work to the conclusion section and discuss it briefly. 5: This study suffers from a fresh literature review. It is recommended to boost the literature review of this study. 6: Please add the system specifications used for the evaluation as well as the programming language. 7: There are some typos and grammatical errors that should be corrected. Reviewer #2: Summary: In this work, COVID-19 case data have been collected from around the world. The regions of waves are labelled. Also, XGBoost model is used to provide a minimum standard for future classifiers trained on this dataset. In addition, the utility of the dataset for the prediction of (future) waves. The manuscript is interesting; however, the following comment should be addressed : Abstract : - - - - - - - - - - - 1 – Some facts about the collected dataset need to be included in the abstract. Introduction Section : - - - - - - - - - - - - - - - - - - - - - - 2 – The introduction need to be extended because it is very short. 3 – The contribution should be included as a list at the end of the introduction section . Data and Methods Section : - - - - - - - - - - - - - - - - - - - - - - - - 4 – This section is fine. No comments. The Datasets Section : - - - - - - - - - - - - - - - - - - - - - - 5 – More details about the dataset should be included . 6 – Visual analysis should be discussed thoroughly . Results Section : - - - - - - - - - - - - - - - - - - - - - - 7 – The author mentioned that supervised classifier can be used. Thus , the author need to refer to other types of feature extraction tools. For example: a) 10.1109/ACCESS.2022.3170893, b) 10.1002/cpe.7311, and c) 10.3390/sym14040715 . Conclusion Section : - - - - - - - - - - - - - - - - - - - - - - 8 – This section is fine. No comments . General Comments: - - - - - - - - - - - - - - - - - 9 - There are some grammatical errors that should be corrected . It is highly recommended to be proofed the manuscript carefully . - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ****** 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. https://doi.org/10.1371/journal.pone.0284076.r001
Revision 1
10 Jan 2023 Author Response Response to Reviewer 1 1. All the sections and subsections must be included in the text, Such as :( Data and Methods, Smoothing Algorithms, etc.). We have added all sections and subsections. Further, we have now (slightly) reorganized the sections and subsections for better readability. 2. The abstract needs to be improved to do justice to the main contributions of the paper, also it contains some abbreviations that need to be explained. We have improved the abstract, with more details regarding the contributions made, the nature of the dataset created, and the baseline classifiers. All abbreviations used in the abstract, have also been explained. 3. The contribution is not stated also add it at the end of the introduction section. We have added the contributions in the Introduction section (lines xx-yy). 4. This study suffers from a fresh literature review. It is recommended to boost the literature review of this study. We have now included an additional paragraph in the “Introduction” section to boost the literature review, as per the reviewer’s suggestion (lines 8-13). 5. Please add the system specifications used for the evaluation as well as the programming language. Since we are not reporting any runtimes, we have not reported system specifications. We have now clearly indicated the programming language, and that the codes were run on Google Colaboratory, at the beginning of the Data and Methods section (lines 28-32). 6. This study suffers from a fresh literature review. It is recommended to boost the literature review of this study. We have now extended the Introduction section, with some methods of predicting COVID waves (lines 8-16). 7. There are some typos and grammatical errors that should be corrected. We have carefully proofread the document again, and corrected all typos and grammatical errors that were found. Response to Reviewer 2: 1. Some facts about the collected dataset need to be included in the abstract. We have added the source of the initially collected dataset, in the abstract. 2. The introduction needs to be extended because it is very short. We have now extended the Introduction section, with some methods of predicting COVID waves. 3. The contribution should be included as a list at the end of the introduction section. We have included the contribution at the end of the introduction (lines 18-21). 4. This section is fine. No comments. We thank the reviewer for their appreciation. 5. More details about the dataset should be included. We have now included more details about the dataset used to build the COWAVE datasets. 6. Visual analysis should be discussed thoroughly. We have improved the discussion of the visual analysis. 7. The author mentioned that a supervised classifier can be used. Thus, the author needs to refer to other types of feature extraction tools. For example: a) 10.1109/ACCESS.2022.3170893, b) 10.1002/cpe.7311, and c) 10.3390/sym14040715. We have now cited other possible feature selection techniques (lines 223-224). 8. This section is fine. No comments. We thank the reviewer for their appreciation. 9. There are some grammatical errors that should be corrected. It is highly recommended to be proofed the manuscript carefully. We have carefully proofread the document again and corrected all typos and grammatical errors that were found. https://doi.org/10.1371/journal.pone.0284076.r002
24 Mar 2023 Decision Letter - Hilal Tayara, Editor COWAVE: A Labelled COVID-19 Wave Dataset for Building Predictive Models PONE-D-22-27577R1 Dear Dr. Raman, 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, Hilal Tayara Academic Editor PLOS ONE Additional Editor Comments (optional): Please address all comments raised by reviewr 4. 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: All comments have been addressed Reviewer #4: (No Response) Reviewer #5: All comments have been addressed Reviewer #6: 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 #2: Yes Reviewer #3: Yes Reviewer #4: (No Response) Reviewer #5: Yes Reviewer #6: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes Reviewer #3: Yes Reviewer #4: (No Response) Reviewer #5: Yes Reviewer #6: 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 Reviewer #4: (No Response) Reviewer #5: Yes Reviewer #6: 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 Reviewer #4: (No Response) Reviewer #5: Yes Reviewer #6: 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: Summary: In this work, COVID-19 case data have been collected from around the world. The regions of waves are labelled. Also, XGBoost model is used to provide a minimum standard for future classifiers trained on this dataset. In addition, the utility of the dataset for the prediction of (future) waves. The authors have addressed the raised comments. Comments : Abstract : - - - - - - - - - - - 1 – The abstract is fine. No further comments . Introduction Section : - - - - - - - - - - - - - - - - - - - - - - 2 – This section is fine. No further comments . Data and Methods Section : - - - - - - - - - - - - - - - - - - - - - - - - 3 – This section is fine. No further comments . Results Section : - - - - - - - - - - - - - - - - - - - - - - 4 – This section is fine. No further comments . Conclusion Section : - - - - - - - - - - - - - - - - - - - - - - 5 – This section is fine. No further comments . - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Reviewer #3: This version of the manuscript is well improved. The authors have addressed all reviewer comments. The manuscript can be accepted for publication. Reviewer #4: - The abstract is long and NOT satisfactory. It should contain the following parts: i. The importance of or motivation for the research. ii. The issue/argument of the research. iii. The methodology. iv. The result/findings. v. The implications of the result/findings. -where is keyword list.Authors should add keyword list contain of 5 to 8 keywords. -The motivation and contribution need to be improve in introduction.Author should also add seprate paragaraph of orgnization at the end of introducation. -Was the dataset balanced? if the dataset is unbalanced and may affect the results significantly. The authors should solve the problem of the unbalanced dataset. -Clearly highlight the mathematical terms used in the paper and explain them in the text. -Author should discuss more recent reference in introducation COVID-19 detection by dogs: From physiology to field application-a review article Combination of Angiotensin (1-7) Agonists and Convalescent Plasma as a New Strategy to Overcome Angiotensin Converting Enzyme 2 (ACE2) Inhibition for the Treatment of COVID-19 Derivatization and combination therapy of current COVID-19 therapeutic agents: a review of mechanistic pathways, adverse effects, and binding sites The next frontier in vaccine safety and VAERS: Lessons from COVID-19 and ten recommendations for action - Conclusion to be made more systematic and future scope to be elaborated more on technical features that are planned to be added in the proposed system in the near future. - The use of English language is fine, however, it is recommended to be checked once again. Reviewer #5: The authors have addressed all the comments. The manuscript is well structured. Abstract is okay. data collection, Methodology, results and discussion are okay. Relevant articles were cited and properly referenced. Reviewer #6: (No Response) ******** 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 Reviewer #4: No Reviewer #5: Yes: Boluwaji Ade Akinnuwesi Reviewer #6: No ******** https://doi.org/10.1371/journal.pone.0284076.r003
Formally Accepted
3 Apr 2023 Acceptance Letter - Hilal Tayara, Editor PONE-D-22-27577R1 COWAVE: A Labelled COVID-19 Wave Dataset for Building Predictive Models Dear Dr. Raman: 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 Dr. Hilal Tayara Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0284076.r004

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