Peer Review History
Original SubmissionMay 14, 2020 |
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Transfer Alert
This paper was transferred from another journal. As a result, its full editorial history (including decision letters, peer reviews and author responses) may not be present.
PONE-D-20-14374 Multivariable prediction model of ICU transfer and death: a French prospective cohort study of COVID-19 patients. PLOS ONE Dear Dr. Maalouf, Your submission has now been peer-reviewed by two experts in the field and myself. I agree that the manuscript would benefit from being revised according to the suggestions following and encourage you to do so. I have read with great interest your manuscript and firmly believe that it contributes to a better understanding of the Covid situation. However, I should point out that several methodological flaws exist and would suggest revising accordingly. Title:
Abstract:
Methods
Discussion
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We will update your Data Availability statement on your behalf to reflect the information you provide 7. One of the noted authors is a group or consortium; DIMICOVID. In addition to naming the author group, please list the individual authors and affiliations within this group in the acknowledgments section of your manuscript. Please also indicate clearly a lead author for this group along with a contact email address. 8. Please amend either the abstract on the online submission form (via Edit Submission) or the abstract in the manuscript so that they are identical. [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: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know 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: No 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: Thank you for the opportunity to review this work. I believe there is currently a great demand for prognostic models for COVID-19. The authors have developed a novel prediction score with a population of 152 adults with COVID-19. They conducted validation internally using bootstrapping, and with an external cohort of 131 patients recruited at another hospital. The authors list three outcomes of interest, but their main focus appears to be ICU admission or death within 14 days. A key concern is the number of events described. In their development sample, 47 people died or were admitted to ICU, and in the validation sample 36. Collins et al. recommend at least 100 and ideally 200 to validate a prognostic model (https://doi.org/10.1002/sim.6787). It would be ideal if the authors were able to validate their score in a sample of this size. If not, the discussion should draw readers’ attention to this issue, and advise caution before this score is used. I would like to see more details in the main manuscript on the methods used to develop the score. Particular issues are: 1. In univariable analyses, 21 variables are significantly related to ICU admission or death. How were the four included in the multivariable analysis chosen? 2. How were the variables in the multivariable model converted into the score? Of especial note is that CRP is responsible for 3 out of 8 possible points in the score but was statistically non-significant in the multivariable analysis for the outcome of ICU admission or death. 3. There are three different models described in the supplement for the three different outcomes. I think the manuscript needs to be clear what outcome the score is intended to predict. 4. For the calibration curves, it is unclear which model the predicted values come from. Oxygen requirement, particularly non-invasive ventilation, is included as a risk factor and as a component in the prediction score, and is also treated as an outcome. While I appreciate that these are at different timepoints, I think this needs to be addressed in the discussion. Could the authors provide more detail about the validation cohort please? Were data collected for this validation or for another purpose? Are there any differences between the cohorts (e.g. different size hospital, recruited at different time in the epidemic) or differences in data collection and follow-up? Any missing data in the validation cohort? It might help to add a second panel to Figure 1 with details of the validation cohort. The methods state that missing data were described with a count, but these do not appear to be reported. Figure 1. It would be clearer to have a box showing excluded patients, then the number included in the analysis, rather than the footnote. There are 6 patients who do not have 14 days of follow-up. The one admitted to ICU appears to be included in the analysis but the other five not. Figure 2. The caption for Figure 2 describes a forest plot, but no forest plot is included in the PDF. Figure 4 shows time-to-event details, but no time-to-event analyses are discussed. I think it would be clearer to show the calibration plots here, or possibly a receiver operating characteristic curve. The discussion references other prognostic scores for COVID-19. It would help readers to describe how this novel score compares to those. It would also be useful to see how the authors anticipate the score being used. They have identified three risk levels. It would be useful to see positive- and negative-predictive values for these thresholds. I would also like more details in the discussion of how the authors anticipate that these levels should be used (keeping in mind the initial concern regarding validation with a larger dataset). Minor comments: 1. The WHO scale described is a 9-point scale, not 8. 2. The text on page 8 states ‘more than half showing values below 800 cells’, but the table gives this proportion as 48% 3. Typo in Table 1 ventricule for ventricle 4. Typos on page 14: presente for present (twice) 5. Typo halfway down page 15 ‘probability N of’ 6. Typo of VNI for NIV in the supplementary table 7. Could the authors please define ‘high flow oxygen’ as a flow rate so this is unambiguous for international readers who might want to apply the score. Reviewer #2: Major comments 1. It is well-known that, in prognostic cohort studies, it is important to have an adequate sample size when developing a prediction model. A larger sample size will yield more findings of high reliability. Although what constitutes an “adequate” sample size is a difficult question, some results there exist in the literature. From this point of view the authors should verify if their study meets the rule(s) of thumb suggested in: -- Peduzzi P, Concato J, Kemper E, Holford TR, Feinstein AR. A simulation study of the number of events per variable in logistic regression analysis. J Clin Epidemiol 1996; 49:1373-1379 2. The authors should discuss the important multicollinearity issue. 3. The authors say that missing data were described with count, but the way they are dealt with in the regression analysis is unclear. The authors should discuss this aspect. 4. In addition to calibration and discrimination, the authors should evaluate the strength of the predictions from the model. In these terms, measures of performance (not of association) are needed. For binary outcomes, recently proposed R2 or Brier score can be used to present overall performance measures; see -- Nagelkerke NJ. A note on a general definition of the coefficient of determination. Biometrika 1991; 78:691-692 -- Tjur T. Coefficients of determination in logistic regression models—A new proposal: the coefficient of discrimination. Am Stat 2009; 63;366-372 -- Rufibach K. Use of Brier score to assess binary predictions. J Clin Epidemiol 2010; 63:938-939 Minor comments 1. The symbol “n” for the sample size is used but never defined. Moreover, it is not in italic. Please check. 2. The authors write: “Categorical variables were compared using Fisher’s exact test and quantitative variable with Wilcoxon’s rank sum test.” I think it should be more correct to say that: “The association/dependence between variables was evaluated using Fisher’s exact test for categorical variables, and with Wilcoxon’s rank sum test for quantitative variables.” ********** 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. 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Revision 1 |
Development of a multivariate prediction model of intensive care unit transfer or death: A French prospective cohort study of hospitalized COVID-19 patients PONE-D-20-14374R1 Dear Dr. Maalouf, Thank you for submitting your article to PLoS One, which I have pleasure in accepting for publication as an original research paper. Well done and many congratulations! Your manuscript has now been formally accepted for publication. Please see important details concerning the publication process below. Your efforts during the process of revision are acknowledged and I hope you also are pleased with the final result. We appreciate being able to publish your work and look forward to seeing your paper online as soon as possible. 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, José Moreira, MD, MSc Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
Formally Accepted |
PONE-D-20-14374R1 Development of a multivariate prediction model of intensive care unit transfer or death: A French prospective cohort study of hospitalized COVID-19 patients Dear Dr. Maalouf: 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. José Moreira Academic Editor PLOS ONE |
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