Pooled prevalence of stunting and associated factors among children aged 6–59 months in Sub-Saharan Africa countries: A Bayesian multilevel approach

Bayley Adane Takele; Lemma Derseh Gezie; Tesfa Sewunet Alamneh

doi:10.1371/journal.pone.0275889

Peer Review History

Original SubmissionSeptember 4, 2021
17 May 2022 Decision Letter - Orvalho Augusto, Editor PONE-D-21-28714Pooled Prevalence of Stunting and Associated Factors among Children Aged 6-59 Months in Sub-Saharan Africa Countries: A Bayesian multilevel approachPLOS ONE Dear Dr. Adane, 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 01 2022 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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Additional Editor Comments: The authors estimate a common prevalence in sub-Saharan Africa using 35 DHS surveys conducted between 2008 and 2018. As expected they found a very high prevalence across the continent and similar factors and conclusions as previously published analyses have shown. The only new information from this analysis is that there remains a large unexplained variance given their heterogeneity measures (ICC, MOR etc). We know that stunting is not spread all over the country. There are pockets of it in a country. So, why not a sub-country prevalence pooling? That would help more each country to act. I would suggest the authors to at least discuss this. Major issues: 1. Introduction/Background Please cut this current introduction to something close the half of what it is now. Please ensure a flowing text. Eg: Remove the Bayesian argument in the background (you may put part of it in the methods); avoid orphan statements like “Globally, approximately 155 million children under five suffer from stunting” and the “A cross-sectional study conducted using evidence from thirty-five …” 2. Statistical analysis In a very confusing way, the authors mention survey sampling analysis with Stata (I guess to compute prevalence which was synthesized into the forest plot in figure 1) and child individual-level analysis with brms/R (for the analysis of factors). This must be clarified: - For the prevalence pooling please i) put details on how country-level prevalence was estimated, not just throw software name (eg: state at least what kind of variance estimator are using for the proportions here). ii) please add information on how the synthetization happened (inverse variance weighting? Random-effects modelling? Logit transformation? Etc etc… what software was used here? It seems to be Stata). - For Bayesian analysis and factors study: Reduce the text please. Lots of what is written is “jargon” of Bayesian arguments. You can move a lot of this to supplementary materials. For example: You put a very general prior consideration but no information of the priors used in this analysis! 3. The discussion in the limitations fails to recognize that you do not have health systems, governance and particular high-level country and region variables. Minor issues: 1. Please cite the software you use: Stata R And brms as an R library/package. This is critical to cite the paper from Paul-Christian Bürkne. 2. Table 1 and 2 could be placed together. And in the supplementary materials we should have it per survey. 3. Figure 1 needs more work. - Prevalence will never be negative. So why are negative labels there? [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: I Don't Know ****** 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. 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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Thank you very much for submitting this manuscript. This is one of the important topics to improve child survival in Sub-Saharan Africa. Following are my comments/suggestions: 1. Abstract: 1.1. In methods, kindly give the duration of DHS datasets. 1.2. In the results, there are several grammatic errors, please correct these. 1.3. Your conclusion is not according to the results presented in the results. Kindly correct it. 2. Main manuscript: 2.1. Background: Very long and it is not presented well. Usually, the background should depict epidemiology, what is known, what is unknown and how this research generates evidence to fill the gap in knowledge. kindly rewrite the background. 2.2. Methods: you have stated, .."In 2015, Sub-Saharan Africa was home to 27 of the world’s 28 poorest countries and had more extremely poor people than in the rest of the world combined." Kindly give a reference to support this statement. 2.3. Methods: Individual-level variables - Why breastfeeding was not mentioned here. Please explain whether you used ever breastfed and currently breastfeeding? further, complementary feeding is very important. Why you did not use this in the final model. please consider this variable to improve the current analysis. 2.4. Methods: You stated, "These datasets were appended, cleaned, and recoded according....." Please explain how did you clean the data. Write all the steps of DHS data cleaning once you downloaded the dataset from the public domain. 2.5. Results: Table 1: Please be consistent with decimal points. 2.6. Results: Table 2: Place of delivery; kindly use skilled or skilled birth attendants also. 2.7. Results: Figure 1: Please explain the analysis you have done for Figure 1 in the method section. it seems you used meta-analysis. 2.8. Results: Table 3: Child age: please explain this in the text. 2.9. Results: Table 3: Kindly change the reference value of maternal age to show the risk factor for stunting. 2.10. Results: Table 3: SSA regions - East Africa, in the adjusted community-level model it shows a protective effect while in the full model t is one of the risk factors. Please explain it. Further, kindly evaluate the interaction of this variable with any other variable. 2.11. Discussion: Kindly add implications of these findings. 2.12. Discussion: Kindly give a snapshot of the current programmatic efforts in reducing the stunting in East Africa. ****** 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:** Yasir Bin Nisar [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.0275889.r001
Revision 1
10 Aug 2022 Author Response PLOS ONE Point by point response for editors/reviewers comments Manuscript title: Pooled Prevalence of Stunting and Associated Factors among Children Aged 6-59 Months in Sub-Saharan Africa Countries: A Bayesian multilevel approach Manuscript ID: PONE-D-21-28714 Dear editor/reviewer. Dear all, We would like to express our deepest gratitude for this constructive, corrective, and improvable comments, questions and suggestions on this manuscript that would improve the content and scientific merit of the manuscript. We considered each comments and suggestion raised by the editor and reviewer on the manuscript thoroughly. We have performed all of the statistical analyses again and addressed all the editor’s and reviewer’s comments in our revised manuscript (both with track changes and without track changes). Our point-by-point responses for each comments and questions are described in bold referenced by page/line of the resubmission. Response to Editor’s comment Additional comments Authors’ response: We Thank the editor for this interesting comment and we sense the issue raised. But there are plenty of studies that estimates sub-country level stunting prevalence rather the aim of this study was to determine the burden of stunting at regional and sub-regional level which inturn could enable international, regional and sub-regional organizations, and other stakeholders to cooperate and share good experiences to accelerate the staggering reduction of stunting of children in SSA (See Background section, line 104, page 5). Major issues: 1. Introduction/Background Please cut this current introduction to something close the half of what it is now. Please ensure a flowing text. Eg: Remove the Bayesian argument in the background (you may put part of it in the methods); avoid orphan statements like “Globally, approximately 155 million children under five suffer from stunting” and the “A cross-sectional study conducted using evidence from thirty-five…” Authors’ response: Thank you for the comments. We accepted and modified it accordingly. (See Background section, page 4-5 ). 2. Statistical analysis In a very confusing way, the authors mention survey sampling analysis with Stata (I guess to compute prevalence which was synthesized into the forest plot in figure 1) and child individual-level analysis with brms/R (for the analysis of factors). This must be clarified: - For the prevalence pooling please i) put details on how country-level prevalence was estimated, not just throw software name (eg: state at least what kind of variance estimator are using for the proportions here). ii) please add information on how the synthetization happened (inverse variance weighting? Random-effects modelling? Logit transformation? Etc etc… what software was used here? It seems to be Stata). -For Bayesian analysis and factors study: Reduce the text please. Lots of what is written is “jargon” of Bayesian arguments. You can move a lot of this to supplementary materials. For example: You put a very general prior consideration but no information of the priors used in this analysis! Authors’ response: Thank you for the concerns. We accepted and modified it. (see statistical analysis section, page 9-11, and supplementary materials). 3. The discussion in the limitations fails to recognize that you do not have health systems, governance and particular high-level country and region variables. Authors’ response: Thank you for the comment. We accepted and included it. (see strength and limitation section of the discussion, line 492, page 22). Minor issues: 1. Please site the software you use; Stata, R and brms as an R library/package. This is critical to cite the paper from Paul-Christian Bürkne. Authors’ response: Thank you for the concerns. We modified it accordingly. (see data management and analysis of the methods section, line 175, page 8). 2. Table 1 and 2 could be placed together. And in the supplementary materials we should have it per survey Authors’ response: Thank you for the comment. We accepted and modified it accordingly. (see Table 1, page 29-30, and the supplementary materials). 3. Figure 1 needs more work. Prevalence will never be negative. So why are negative labels there? Authors’ response: Thank you for the careful notice of the figure and identifying the issue. We accepted and modified it accordingly. (see Figure 1). Response to reviewers comments 1. Abstract 1.1 In methods, kindly give the duration of DHS datasets. Authors’ response: Thank you for the comments. We accepted and modified it. (See Abstract section, line 44, page 2). 1.2. In the results, there are several grammatic errors, please correct these. Authors’ response: Thank you for the concerns. We corrected it in the revised manuscript. (See Result section of the abstract, line 50, page 3). 1.3. Your conclusion is not according to the results presented in the results. Kindly correct it. Authors’ response: Thank you for the comments. We corrected it in the revised manuscript (see Conclusion part of the abstract, line 56, page 3). 2. Main manuscript: 2.1 Background:Very long and it is not presented well. Usually, the background should depict epidemiology, what is known, what is unknown and how this research generates evidence to fill the gap in knowledge. kindly rewrite the background. Authors’ response: Thank you for the comments . We accepted and addressed it in the revised manuscript (see Background section, line 62, page 4). 2.2. Methods: you have stated, .."In 2015, Sub-Saharan Africa was home to 27 of the world’s 28 poorest countries and had more extremely poor people than in the rest of the world combined." Kindly give a reference to support this statement. Authors’ response: Thank you for the comments . We addressed it in the revised manuscript (see Methods section, line, 119, page 6). 2.3. Methods: Individual-level variables - Why breastfeeding was not mentioned here. Please explain whether you used ever breastfed and currently breastfeeding? further, complementary feeding is very important. Why you did not use this in the final model. please consider this variable to improve the current analysis. Authors’ response: Thank you for the concerns. Dear reviewers, regarding breast feeding we addressed it in the revised manuscript (see Methods section, line 161, page 8). Regarding complementary feeding, it was one of our candidate explanatory variables but we had dropped it because of its high multicollinearity (VIF>10). 2.4. Methods: You stated, "These datasets were appended, cleaned, and recoded according....." Please explain how did you clean the data. Write all the steps of DHS data cleaning once you downloaded the dataset from the public domain. Authors’ response: Thank you for the comments . We addressed it in the revised manuscript (see Methods section, line 162 page 8). 2.5. Results: Table 1: Please be consistent with decimal points. Authors’ response: Thank you for the observations. We corrected it in the revised manuscript (see Results section Table 1, page 29-30). 2.6. Results: Table 2: Place of delivery; kindly use skilled or skilled birth attendants also. Authors’ response: Thank you for the concern. Skill birth attendants was one of our candidate explanatory variables but we had dropped it from the final model due to its high multicollinearity (VIF>10). 2.7. Results: Figure 1: Please explain the analysis you have done for Figure 1 in the method section. it seems you used meta-analysis. Authors’ response: Thank you for the comment . We accepted and corrected it in the revised manuscript (see Methods section, 174, page 8). 2.8. Results: Table 3: Child age: please explain this in the text. Authors’ response: Thank you for the concern. We explained it accordingly (see Results section, line 307, page 14). 2.9. Results: Table 3: Kindly change the reference value of maternal age to show the risk factor for stunting. Authors’ response: Thank you for the comment. We modified it (see Results section, Table 2, page 32). 2.10. Results: Table 3: SSA regions - East Africa, in the adjusted community-level model it shows a protective effect while in the full model t is one of the risk factors. Please explain it. Further, kindly evaluate the interaction of this variable with any other variable. Authors’ response: Thank you for the concerns. Dear reviewer as you know it very well in multilevel analysis of hierarchical data the interaction between level two and level variables, level two and other level two variables and between level variables are expected, and we authors checked suspected variables for that, and there was no significant interaction effect that is why we have not reported in the manuscript. 2.11. Discussion: Kindly add implications of these findings Authors’ response: Thank you for the comment. We added it (see discussion section, line 476, page 22). 2.12. Discussion: Kindly give a snapshot of the current programmatic efforts in reducing the stunting in East Africa. Authors’ response: Thank you for the comment. We accepted and included it (see discussion section, line 467, page 21). We thank again all reviewers for their helpful critiques that have strengthened this research report! Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0275889.r002
26 Sep 2022 Decision Letter - Orvalho Augusto, Editor Pooled Prevalence of Stunting and Associated Factors among Children Aged 6-59 Months in Sub-Saharan Africa Countries: A Bayesian multilevel approach PONE-D-21-28714R1 Dear Dr. Takele, 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, Orvalho Augusto, MD, MPH 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: (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 #1: Yes: Yasir Bin Nisar ******** https://doi.org/10.1371/journal.pone.0275889.r003
Formally Accepted
3 Oct 2022 Acceptance Letter - Orvalho Augusto, Editor PONE-D-21-28714R1 Pooled Prevalence of Stunting and Associated Factors among Children Aged 6-59 Months in Sub-Saharan Africa Countries: A Bayesian multilevel approach Dear Dr. Takele: 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. Orvalho Augusto Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0275889.r004

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