PONE-D-25-08867Associations among weed communities, management practices, and environmental factors in U.S. snap bean (Phaseolus vulgaris) production

PLOS ONE

Dear Dr. Pavlovic,

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 the introduction section should include reports on successful management of weeds in snap bean production. Also, the authors should explain why a ML random forest approach was selected?

Please submit your revised manuscript by Jun 06 2025 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,

Sumita Acharjee

Academic Editor

PLOS ONE

Journal Requirements:

1. When submitting your revision, we need you to address these additional requirements.

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 your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why.

3. Please note that PLOS ONE has specific guidelines on code sharing for submissions in which author-generated code underpins the findings in the manuscript. In these cases, we expect all author-generated code to be made available without restrictions upon publication of the work. Please review our guidelines at https://journals.plos.org/plosone/s/materials-and-software-sharing#loc-sharing-code and ensure that your code is shared in a way that follows best practice and facilitates reproducibility and reuse.

4. Thank you for stating the following financial disclosure: [This research was funded by U.S. Department of Agriculture–Agricultural Research Service project 5012-12220-010-000D (“Resilience of Integrated Weed Management Systems to Climate Variability in Midwest Crop Production Systems”). Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the U.S. Department of Agriculture. The mention of trade names or commercial products in this publication is solely for the purpose of providing specific information and does not imply recommendation or endorsement. The U.S. Department of Agriculture is an equal opportunity provider and employer.]. 

Please state what role the funders took in the study.  If the funders had no role, please state: ""The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.""

If this statement is not correct you must amend it as needed.

Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf.

5. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data.

6. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information .

7. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[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: This manuscript presents a valuable investigation into the complex interplay between weed communities, management practices, and environmental factors in US snap bean production. The use of machine learning (random forest) to analyze large-scale field survey data represents a robust methodological approach, and the findings offer practical insights for optimizing weed control and yield outcomes. However, several critical areas require improvement to strengthen the study’s validity, interpretability, and alignment with journal standards:

1. While random forest excels in capturing nonlinear relationships, compare its performance against simpler statistical models (e.g., linear regression, GLM) to contextualize its advantages. Present metrics such as R², RMSE, or AIC to justify the choice of machine learning.

2. Acknowledge that your findings are based on mechanized, high-input systems in three US regions. Discuss the limitations to scalability, particularly for smallholder or organic systems where tillage practices, herbicide use, and climate stressors differ. Highlight opportunities to adapt these insights to diverse contexts (e.g., integrating machine learning with low-tech monitoring tools in resource-limited settings).

Specific Comments:

Line 126-131: Why aggregate precipitation into 3 intervals? Justify this choice statistically/methodologically.

Line 132: "machine learning algorithm random forest". Specify "random forest regression" for clarity, as machine learning encompasses diverse methods.

Line 284-293: You attribute NW’s higher yield to "interaction of factors." Elaborate on these factors (e.g., soil moisture, pest pressure).

Line 299-300: The conclusion overstates climate impacts without projecting future scenarios. Recommend adding a brief discussion on how your findings inform adaptive strategies.

Fig 2A. The Northwest (NW) outperforms the Midwest (MW). Could soil type (e.g., sandy vs. clay) or climate adaptation (e.g., heat tolerance) explain this difference?

Reviewer #2: This manuscript presents an analysis on the relationships between management and environmental factors of snap bean fields with crop yield and weed density across the three production regions in the United States collected from survey data using random forest modelling. The authors found region to be the most important predictor of crop yield followed by planting date and whether the producer used row cultivation. Row cultivation and the number of spring tillage operations were the most important predictors of weed density. The introduction does not present a compelling story and could use some reworking. First, it would be beneficial to mention the problem this study addresses earlier rather than in the final paragraph. At first it seems this manuscript will be about shifts in management practices by snap bean producers as the first paragraph does not even mention weeds (or any pest) and most details concern weed impact on bean yields in general and effects of climate change on snap bean and weed management. I think there needs to be greater emphasis on the why here. This is not the first study to link environmental and management practices to weed density and crop yield; have others been successful? Further, why did the authors choose a ML random forest approach? Has this been used to model weed density and crop yield in the past? The methodology and analysis is appropriate for the research question yet no information is provided on why this particular approach was selected. I.e. why random forest modeling and why not another decision tree modeling approach? The results support the conclusions and will be of interest to a wide range of readers. With several small additions I believe this manuscript will be a valuable contribution to PLOS.

L92-94 – How were producers and fields selected for this survey? If it was vegetable processors who were contacted would there be a worry about potential bias?

L100 – If fields were surveyed near harvest time and surveys happened from June to Oct does this mean snap beans are continuously harvested for 5 months? Did the authors survey different regions during different times? I see confounding issues here with sampling over what is essentially the entire growing season.

L104-106 – How were quadrats placed in fields? Were they equally spaced? How did the authors ensure they were capturing variability across the field?

L105 – What is a species group? How did the authors decided which to pool and which not too?

L124-125 – What physical and chemical properties?

L143 – How was weed cover % determined?

L152 – Scaled how?

L153 – Scaled and transformed how?

L175-178 – I think this is important background material missing from the introduction.

L183-186 – What about the authors data?

L198 – On weed populations?

L234 – I think it is obvious different cultivation equipment can cause varying levels of crop damage.

L248 – Is that decline really only 1 plant/m2? It looks closer to 2 but this figure is not easy to interpret. Would a decline in weed density of 1 plant/m2 for row cultivation make it worth it? This seems very low to me.

L297 – Is a 1 plant/m2 decline in weed density a beneficial practice when this is accompanied by yield loss?

All figures are all very low resolution. Please fix.

Figure letter captions are inconsistent, some in top left others in top right, others missing entirely (Fig 3)

Fig 2A, Fig 2C and Fig 4A - are these correct? They only two dots each. Perhaps a box and whisker plot would be better to show distribution of yield and weed density by region and with and without cultivation.

Fig 3 – What is the y-axis on these?

What is the y-axis on Fig 4B? Is it weed density as well? Is this a regression line or just connecting non-continuous points? Further, there is no measure of variability presented.

**********

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.

PONE-D-25-08867R1Associations among weed communities, management practices, and environmental factors in U.S. snap bean (Phaseolus vulgaris) productionPLOS ONE

Dear Dr. Pavlovic,

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.With the reviewers' comments, the revised manuscript is improved compared to the previous version. However, the manuscript needs minor revision, which are indicated below.Please ensure that your decision is justified on PLOS ONE’s publication criteria  and not, for example, on novelty or perceived impact.

Please submit your revised manuscript by Oct 04 2025 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,

Sumita Acharjee

Academic Editor

PLOS ONE

Journal Requirements:

If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

[Note: HTML markup is below. Please do not edit.]

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 #2: (No Response)

**********

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 #2: Yes

**********

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

Reviewer #2: 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 #2: 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 #2: 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 #2: Thank you for addressing nearly all of my comments. One point though regarding two comments.

L104-106 – How were quadrats placed in fields? Were they equally spaced? How did the authors

ensure they were capturing variability across the field?

We have actually provided a reference [19] in L112 to our previously published work and how the

data was collected in those surveys regarding weed populations.

L105 – What is a species group? How did the authors decided which to pool and which not too?

We have actually provided a reference [19] in L112 to our previously published work and how the

data was collected in those surveys regarding weed populations.

Despite this information being available in another published manuscript it is critical for understanding the manuscript under consideration. I think these details should not be omitted.

**********

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 #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.

Associations among weed communities, management practices, and environmental factors in U.S. snap bean (Phaseolus vulgaris) production

PONE-D-25-08867R2

Dear Dr. Pavlovic,

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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager®  and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support .

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,

Sumita Acharjee

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: