How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey

Tom E. Hardwicke; Steven N. Goodman

doi:10.1371/journal.pone.0239598

Peer Review History

Original SubmissionApril 30, 2020
28 May 2020 Decision Letter - Despina Koletsi, Editor PONE-D-20-12128 How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey. PLOS ONE Dear Dr. Goodman, 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 Jul 12 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, Despina Koletsi, Dipl.D.S, MSc, Dr. med. dent, MSc, DLSHTM, PGCHE 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. In order to improve reproducibility and replicability, please provide the list of journals surveyed. Please also provide a statement about whether your sample is representative of a larger population. 3. Thank you for stating the following in the Funding Statement Section of your manuscript: "This work was enabled in part by a fellowship grant to the Meta-Research Innovation Center at Stanford (METRICS) from the Laura and John Arnold Foundation. The Meta-Research Innovation Center Berlin (METRIC-B) is supported by a grant from the Einstein Foundation and Stiftung Charité." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The author(s) received no specific funding for this work." [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 Reviewer #2: Yes ******** 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 conducted a survey to explore how often high impact factor journals in all clinical fields seek statistical expertise for the papers they publish, reasons for not doing so etc. The topic is of general interest and the paper is easy to read. I am afraid I have not many things to say to improve the paper. There are many issues that are addressed to a good extent. I expected the situation to be worse but results may undermine the problem. Partly because missing responses are most probably not missing at random (as reported by the authors) and partly because editors believe unconsiously that the problem is dealt with appropriately. I see a lot of journals asking reviewers whether they have checked the statistical methods or the paper needs someone to check them. No-one checks if the reviewer is knowledgeable of the statistical methods employed in the paper. For example, I am being asked right now by PlosONE "Has the statistical analysis been performed appropriately and rigorously? ". I liked the comment that external statistician may not be aware of certain statistical methods. I also liked the idea of journals hiring statisticians to work full time for them and it is something I have been wandering for quite some time. A solution could be to include a statistician in the author list. Cochrane does this for the systematic reviews it publishes. On the other hand, I am aware of many case where a statistician has been asked to be included in the author list just to show that a statistician was used With the rapid development of easy-to-use software, anyone can do statistical analyses without necessarily understanding its output. The statistical reviewer can probably spot a lot of problems, especially regarding interpretation or methods used but (s)he cannot check whether the method was properly used. As the authors state, the problem is multi-faceted and with the rapidly increasing number of submitted papers and journals emerging, review in general is getting worse. Reviewer #2: I read with great interest they survey by Harwicke and Goodman entitled "How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey.". The manuscript is well written and the findings are clearly presented. I have the following 2 comments: 1) I am wondering whether the authors could namely specify the 107 journals in Supplementary Table 1. 2) Considering the journals included in the current and the initial survey 20 years ago, it would be interesting to see graphically the proportion of changes for specific "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. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0239598.r001
Revision 1
9 Sep 2020 Author Response Memo to: PLoS One editors From: Steven Goodman Re: Response to reviewers Manuscript: PONE-D-20-12128 Title: How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey. Editors Comments: 1.) “In order to improve reproducibility and replicability, please provide the list of journals surveyed. Please also provide a statement about whether your sample is representative of a larger population.” We have provided a complete anonymized datafile, with the computational environment, in the OSF framework, as indicated in the Open Science statement of the paper. However, our IRB approved consent form explicitly stated that we would not identify the journals who answered the survey. We described in detail the sampling frame in lines 59-64: “From the complete list of Web of Science subject categories (228) we identified all 68 sub-domains representing biomedicine. We selected the top 5 journals by impact factor within each sub-domain. We supplemented this list with 68 additional journals previously included in the survey by Goodman and colleagues [22], and assigned each of these to their relevant sub-domain. Finally, we removed any duplicates that appeared in multiple sub-domains. This resulted in a sample of 364 journals.” S file Senate very jazz but everything very engagedupplementary Table 1, included in the manuscript file shows the number of responding journals in each specialty and sub-specialty. This provides the best evidence we can provide relative to the representativeness of the achieved sample. We do not assert that this is perfectly representative of the whole sample; in fact, as we discuss at length in the manuscript, we believe that the sample is likely to be biased towards more statistical review. This only strengthens the findings, because the use of statistical review in this sample is rather low. 2.) Thank you for stating the following in the Funding Statement Section of your manuscript: "This work was enabled in part by a fellowship grant to the Meta-Research Innovation Center at Stanford (METRICS) from the Laura and John Arnold Foundation. The Meta-Research Innovation Center Berlin (METRIC-B) is supported by a grant from the Einstein Foundation and Stiftung Charité." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "The author(s) received no specific funding for this work." Done. Reviewer #1: The authors conducted a survey to explore how often high impact factor journals in all clinical fields seek statistical expertise for the papers they publish, reasons for not doing so etc. The topic is of general interest and the paper is easy to read. I am afraid I have not many things to say to improve the paper. There are many issues that are addressed to a good extent…. The reviewer’s comments are appreciated. S/he provides no comments requiring reply or modification of the paper. Reviewer #2: I read with great interest they survey by Hardwicke and Goodman entitled "How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey.". The manuscript is well written and the findings are clearly presented. I have the following 2 comments: 1) I am wondering whether the authors could namely specify the 107 journals in Supplementary Table 1. For the reasons provided in the response to the editor's comments, we unfortunately cannot do this; the journals were promised confidentiality. mood 2) Considering the journals included in the current and the initial survey 20 years ago, it would be interesting to see graphically the proportion of changes for specific "variables". Unfortunately, we no longer have the data files from the survey 20 years ago. We would have liked to have been able to conduct the same analysis, but we couldn't. Attachments Attachment Submitted filename: Response to reviewers.docx https://doi.org/10.1371/journal.pone.0239598.r002
10 Sep 2020 Decision Letter - Despina Koletsi, Editor How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey. PONE-D-20-12128R1 Dear Dr. Goodman, 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, Despina Koletsi, Dipl.D.S, MSc, Dr. med. dent, MSc, DLSHTM, PGCHEd Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0239598.r003
Formally Accepted
23 Sep 2020 Acceptance Letter - Despina Koletsi, Editor PONE-D-20-12128R1 How often do leading biomedical journals use statistical experts to evaluate statistical methods? The results of a survey. Dear Dr. Goodman: 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. Despina Koletsi Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0239598.r004

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