Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using a constrained mixture design and surface response approach

André Sradnick; Marie Werner; Oliver Körner

doi:10.1371/journal.pone.0289320

Peer Review History

Original SubmissionMarch 27, 2023
3 May 2023 Decision Letter - Randall P. Niedz, Editor PONE-D-23-09146Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using an extreme vertices design and surface response approach PLOS ONE Dear Dr. Sradnick, 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 Jun 17 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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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 note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 3. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ Additional Editor Comments: Greater clarity and additional information are required. Because mixture designs, and in particular constrained mixture designs, are not commonly used it would be very helpful to the reader to provide additional detail. I suggest the following - 1) The design matrices used. Include in the materials section. Be very explicit when describing the designs - e.g., a 5-component mixture that included .... Maybe include a small table that provides the proportional ranges for each component. 2) ANOVAs for all measured responses. I did not see any ANOVAs. Most of these would be in the supplement but the salient effects would be included in the manuscript. This might take some thought as time was included. Time could have been added as a process variable, but because it was not maybe select the end timepoint for the ANOVAs presented in the text. 3) Describe the data and model quality diagnostics used in the materials section. E.g., how was data analyzed to determine if a transform was required? These analyses would be in the Results section. 4) Because mixture effects are very different conceptually from amount effects, include trace plots (the standard way to illustrate mixture component effects) of the salient effects. Was there nonlinear blending? This is precisely what mixture effects can detect that factorials cannot. Nonlinear blending determines whether synergies or antagonistic effects were detected. 5) I would tend to not use the term "extreme vertices" but rather constrained as it is more intuitive to the reader not as familiar with mixture concepts. 6) Restructure the text to include the above. [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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: No 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: No ****** 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: I have completed my evaluation of the manuscript intituled: Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using an extreme vertices design and surface response approach. The work presented by the authors is very interesting. I agree to the publication, and the justifications are: The abstract is clearly presented and are related to the data presented in the results section. The introduction provides sufficient information about the subject addressed. Materials and methods are adequately described; The overall value of the manuscript is excellent, but the presentation needs a detailed correction: In figures 2 and 3, the numbers inside the figure's white triangle are unclear. Please, edit the figure to show the numbers clearly. Reviewer #2: I have reviewed the manuscript titled “Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using an extreme vertices design and surface response approach”, and overall, I find the work to be promising. However, I have some concerns regarding the presentation of the results. In my opinion, the results section is poorly structured, and it is challenging for the reader to follow the logical flow of the study. This is the biggest problem. The authors should carefully consider improving this section. The captions for the tables and figures are not informative enough, and it is difficult to understand the data without having to go back to the main text. Additionally, the manuscript uses several abbreviations and short forms for terminologies, which are not adequately explained or defined in the text (Section Experimental Design starting with line 139). Furthermore, the naming of mixtures using the letter M is of course reasonable and should be implemented throughout the tables as well. Overall, I believe that the manuscript has the potential to make a significant contribution to the field, and I recommend it for publication after the necessary revisions have been made. ****** 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.0289320.r001
Revision 1
17 Jun 2023 Author Response PONE-D-23-09146 Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using an extreme vertices design and surface response approach Additional Editor Comments: Greater clarity and additional information are required. Because mixture designs, and in particular constrained mixture designs, are not commonly used it would be very helpful to the reader to provide additional detail. I suggest the following - 1) The design matrices used. Include in the materials section. Be very explicit when describing the designs - e.g., a 5-component mixture that included .... Maybe include a small table that provides the proportional ranges for each component. Response: We have revised the materials and methods part intensively and included two tables (Table 2 and Table 3) for better presentation of the methods (line 102-187). 2) ANOVAs for all measured responses. I did not see any ANOVAs. Most of these would be in the supplement but the salient effects would be included in the manuscript. Response: Thank you for the advice. We have been added the CD (critical distance: confidence interval from TukeyHSD / 2) after ANOVA in the supplement to prevent clarity of the tables (please look at Tables S1 table 1 and S2 table 2) . Several adaptions are made in results part too (line 192-283). This might take some thought as time was included. Time could have been added as a process variable, but because it was not maybe select the end timepoint for the ANOVAs presented in the text. Response: Apologies for the discrepancy in the results section where it was mistakenly stated that the time effect was determined through a test. Due to the nature of the experimental design, the time steps were not independent. To ensure clarity, we have made intensive revisions to all parts of the results section (line 197-294). 3) Describe the data and model quality diagnostics used in the materials section. E.g., how was data analyzed to determine if a transform was required? Response: We have been testing the all-data for homogeneity of variances by three means: Levene’s test, Shapiro-Wilk test and Durbin-Watson test. To our satisfaction (and indeed somewhat surprisingly) all datasets have passed all three tests. We have thoroughly double-checked the data and R-coding, and it is all correct. Due that and according to the statistical rules no adaption was required. Additional information was added in line: 164-167. These analyses would be in the Results section. Response: The results section was extensively revised (line 197-294) 4) Because mixture effects are very different conceptually from amount effects, include trace plots (the standard way to illustrate mixture component effects) of the salient effects. Response: Thanks for this helpful hint, we have determined for the main datasets "Piepel direktions" and added them to the supplementary (S7-S8). Was there nonlinear blending? This is precisely what mixture effects can detect that factorials cannot. Nonlinear blending determines whether synergies or antagonistic effects were detected. Response: Thank you for this important note. In addition to the linear model, the data sets were also tested for quadratic relationships. Here, interaction effects were mostly very weak. Likewise, the variance inflation factor (VIF) increased to such an extent that the uncertainty for the parameters shown is too pronounced. 5) I would tend to not use the term "extreme vertices" but rather constrained as it is more intuitive to the reader not as familiar with mixture concepts. Response: Thank you for the hint. “Extreme vertexes design” is converted to:“constrained mixture design” 6) Restructure the text to include the above. Reviewer #1: I have completed my evaluation of the manuscript intituled: Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using an extreme vertices design and surface response approach. The work presented by the authors is very interesting. I agree to the publication, and the justifications are: The abstract is clearly presented and are related to the data presented in the results section. The introduction provides sufficient information about the subject addressed. Materials and methods are adequately described; The overall value of the manuscript is excellent, but the presentation needs a detailed correction: In figures 2 and 3, the numbers inside the figure's white triangle are unclear. Please, edit the figure to show the numbers clearly. Response: We have modified the figures in order to make the displayed numbers in the illustrations more visible (see Fig2 and Fig3). Reviewer #2: I have reviewed the manuscript titled “Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using an extreme vertices design and surface response approach”, and overall, I find the work to be promising. However, I have some concerns regarding the presentation of the results. In my opinion, the results section is poorly structured, and it is challenging for the reader to follow the logical flow of the study. This is the biggest problem. The authors should carefully consider improving this section. Response: Thank you very much for the comment. The results section has been intensively edited and strongly rewritten to make the measurement data clearer. Line: 198-298. The captions for the tables and figures are not informative enough, and it is difficult to understand the data without having to go back to the main text. All table and figure captions have been revised to facilitate interpretation of the results (see, line 633-656, Table 1-5 and line 291-298). Additionally, the manuscript uses several abbreviations and short forms for terminologies, which are not adequately explained or defined in the text (Section Experimental Design starting with line 139). Response: Thank you very much for the hint. The text has been revised in line with your comment (line 106-109). Furthermore, the naming of mixtures using the letter M is of course reasonable and should be implemented throughout the tables as well. Response: The tables in the supplementary now have the designation M1-MX. Table2 and table S1-S2 Overall, I believe that the manuscript has the potential to make a significant contribution to the field, and I recommend it for publication after the necessary revisions have been made.________________________________________ Attachments Attachment Submitted filename: Reviewer_responce 20230613.docx https://doi.org/10.1371/journal.pone.0289320.r002
17 Jul 2023 Decision Letter - Randall P. Niedz, Editor Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using a constrained mixture design and surface response approach PONE-D-23-09146R1 Dear Dr. Sradnick, 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, Randall P. Niedz Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0289320.r003
Formally Accepted
21 Jul 2023 Acceptance Letter - Randall P. Niedz, Editor PONE-D-23-09146R1 Make a choice: A rapid strategy for minimizing peat in horticultural press pots substrates using a constrained mixture design and surface response approach Dear Dr. Sradnick: 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. Randall P. Niedz Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0289320.r004

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