PONE-D-21-24626Learning how a tree branches out: A statistical approachPLOS ONE

Dear Dr. Rivest,

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, in particular the points raised by the first reviewer. 

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Kind regards,

Esmaiel Jabbari, PhD

Academic Editor

PLOS ONE

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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: No

Reviewer #2: Yes

Reviewer #3: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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

Reviewer #3: Yes

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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: To understand this paper one needs to have read Dutilleul et al. (2015). A subset of three trees are used here. CT (computerized tomography) seems to be limited to just ‘miniature’ trees (ca. 20 cm tall and wide). Is there any reason to believe that, ontologically, such models will apply to mature trees? It is difficult to see what this work seeks to achieve apart from applying CT scanning to very small trees. Further, the new paper seems to be a rerun of the earlier search for internal patterns to branching with fractal analysis, one that now looks for statistical correlations.

A main concern is what is meant by a ‘sample’ in this paper. From my reading, the whole tree is scanned to obtain a complete skeletal structure (e.g. Fig. 1a). This not a sample in the statistical sense. In other words, the data analysis does not use repeatedly-taken random samples of branches (and sub-branches) but all the information about each tree is taken together. Since statistical distributions are applied to model the error terms (as part of the different regression fitting), using all data per tree means surely that the individual (derived) values are not independent (see Table 1). They are very highly likely to be spatially autocorrelated. Unless, I have overlooked something, or there is a part missing to the paper, the application of regression and statistical inference cannot be valid. I could find no discussion by the authors of ‘sampling’, ‘independence’ or ‘randomization’. On line 225, ‘sample means’ and ‘sample standard deviations’ are referred to. Examining the data frames in the DMRSuppMat.zip files it would indeed appear that all data are involved after the line-segment conversion. On line 181 it is said that there are ‘eleven underlying random variables’, which left me more confused. Furthermore, how can it be justified that a conditional variable becomes an explanatory one? Much more explanation of the rational is needed. Important issues concerning causality are involved and need addressing.

The main outcome of this analysis is given on lines 305-313: that level 2 branch variables are the most important to tree form. But this will not be a surprise to many plant scientists given that major 1-D segments are being distributed (placed) within a 3-D volume (or, when more constrained, onto a 2-D plane). And that level 4 branch variables depend upon the level 2 ones, but not on those of level 3, is not really “intriguing”, at least to me, rather it is counterintuitive to what we know of the physiology and development of growing trees. Surely this aspect needs to be unravelled and fully investigated before publishing? Perhaps this ‘odd’ result occurs because of a mix of positive and negative correlations between variables which have a spatial auto-correlative component?

In conclusion, reading this paper left me dissatisfied and sceptical about both the method and the results. No particular idea or hypothesis was being properly tested. How does such an analysis help advance our understanding of tree architecture and growth? It is more a CT technical applications report.

Minor points:

1. The Abstract has several language errors which lead to misunderstandings. ‘CT’ needs to be defined. The first sentence is not an appropriate way to begin.

2. The Introduction on page 2 has several syntax errors. On line 12, is ‘diverted’ the right word? And, likewise on line 26, is ‘privilege’? In some sentences there are words missing.

3. Figs 1-3 could be easily combined with a common legend.

4. By ‘beta’ distribution I assume (checking the equation in other texts) that ‘beta-binomial’ is meant. It is not explained why this distribution was used to model position x. The beta-binomial is often employed to cater for over-dispersion. Is that the case here? I am unsure that it is the right error distribution and more care is needed to justify it.

5. The conclusion has at least seven spelling errors.

6. Appendices A-E could readily go into the Supplementary Materials files.

Reviewer #2: The authors used modeling and statistical techniques to investigate the branching pattern of trees. The manuscript and data are well organized and presented. This is an interesting approach to analyze trees structure which showed that their branching patterns have various levels of complexity.

Reviewer #3: In this work, branching pattern of trees has been investigated using a statistical modeling technique. The statistical model was fitted to data derived from CT scans of three tree types. I’d recommend accepting the manuscript after the following minor changes.

-Please discuss how the presented method and derived variables/coefficients for three modeled trees could be expanded to other tree types?

-Please discuss how the results will be changed if the modeling is repeated with more trees of the same type. Are the results reported in this work conclusive for three tree types that were investigated, or the model needs to be fitted to more CT data of the same tree type in the future?

-Please discuss the possibility of developing a universal model that accounts for all parameters including tree age and environmental factors.

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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PONE-D-21-24626R1Learning how a tree branches out: A statistical modeling  approachPLOS ONE

Dear Dr. Rivest,

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. In particular:-more in-depth quantitative analysis of branching pattern

Please submit your revised manuscript by Aug 11 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.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Esmaiel Jabbari, PhD

Academic Editor

PLOS ONE

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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 #4: (No Response)

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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 #4: Partly

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #4: No

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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 #4: No

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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 #4: Yes

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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 #4: In the MS "Learning how a tree branches out: A statistical modeling approach," the authors analyzed the data from three small trees. I do believe that this effort could be beneficial, but:

a.- Trees are the dominant life form in all the forests, and understanding their architecture is not only crucial for modeling their photosynthetic capacity. Trees are the minimal habitat for canopy organisms such as epiphytes and insects. In this regard, several authors have tried to test how trees' complexity affects epiphyte diversity, see:

Ruiz-Cordova, J. P., V. H. Toledo-Hernández and A. Flores-Palacios. 2014. The effect of substrate abundance in the vertical stratification of Bromeliad epiphytes in a tropical dry forest (Mexico). Flora 209: 375–384.

Flores-Palacios, A. and J. G. García-Franco. 2006. The relationship between tree size and epiphyte richness: testing four different hypotheses. Journal of Biogeography 33: 323–330.

Victoriano-Romero, E., S. Valencia-Díaz, V. H. Toledo-Hernández and A. Flores-Palacios. 2017. Dispersal limitation of Tillandsia species correlates with rain and host structure in a central Mexican tropical dry forest. PLoS ONE 12(2): e0171614.

At least one of these papers measures most of the tree structures.

b.- All trees have a hierarchy of structures; for example, the first trunk division is not independent of the trunk, and so on. So the different structures and their properties must be modeled considering that they are not independent.

c.- The model description is complex (I understand this), making the replicability of the modeling will be limited. Can you provide a simple r-library for the use of your model? Can you give a single number that will describe branching patterns or tree complexity? If yes, how can this number be used for comparing tree species? Will your model help test ecological hypotheses like those in previous articles?

Join Figures 1, 2, and 3.

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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 #4: Yes: A. Flores-Palacios

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[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.

Learning how a tree branches out: A statistical modeling  approach

PONE-D-21-24626R2

Dear Dr. Rivest,

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,

Esmaiel Jabbari, PhD

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 #4: All comments have been addressed

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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 #4: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #4: 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 #4: Yes

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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 #4: Yes

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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 #4: Thanks for your answers. I think that the impact of the MS will be better if, in the future, you publish an R library with a friendly user’s manual; in this way, you will win many users.

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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 #4: No

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