PONE-D-23-38802Evaluation of a tool to identify risks for tail biting in pigsPLOS ONE

Dear Dr. D'Alessio,

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.

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ACADEMIC EDITOR: Please write a covering letter answering point-by-point the questions posed by the reviewers and mention the page number where the changes are implemented. Additionally, in the manuscript highlight those areas that have undergone changes. 

==============================

Please submit your revised manuscript by Feb 01 2024 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,

Faham Khamesipour, Ph.D.

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 

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2. You indicated that ethical approval was not necessary for your study. We understand that the framework for ethical oversight requirements for studies of this type may differ depending on the setting and we would appreciate some further clarification regarding your research. Could you please provide further details on why your study is exempt from the need for approval and confirmation from your institutional review board or research ethics committee (e.g., in the form of a letter or email correspondence) that ethics review was not necessary for this study? Please include a copy of the correspondence as an ""Other"" file.

3. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. 

When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section.

4. 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.

5. In the online submission form, you indicated that "Data cannot be shared publicly because of GDPR considerations regarding farm audits. Data from the inspections at the abattoir are available upon request (contact via email Keelin.ODriscoll@teagasc.ie) for researchers who meet the criteria for access to confidential data."

All PLOS journals now require all data underlying the findings described in their manuscript to be freely available to other researchers, either 1. In a public repository, 2. Within the manuscript itself, or 3. Uploaded as supplementary information.

This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If your data cannot be made publicly available for ethical or legal reasons (e.g., public availability would compromise patient privacy), please explain your reasons on resubmission and your exemption request will be escalated for approval. 

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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

Reviewer #4: Yes

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

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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: No

Reviewer #2: No

Reviewer #3: No

Reviewer #4: 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: Yes

Reviewer #2: Yes

Reviewer #3: Yes

Reviewer #4: 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: The submitted manuscript describing the evaluation of a tool to identify risks for tail biting in pigs fails to provide data to support the conclusions. The statistical analysis is not well described nor appropriate such that the results cannot be interpreted with any confidence. Therefore, any conclusions are not supported. There appears to be many instances of missing data.

Lines 282-288: the provided descriptive statistics are difficult to understand. Only the second paragraph refers to management practices, so move the heading (4.2 Management practices) and insert an additional heading 4.1 Descriptive statistics.

Example: does Line 283 indicate that the finisher stage sample population was 85 pens with 37.4±58.6 pigs/pen?

Example: what do the Line 287 numbers after 6421 and Line 288 numbers after 7197 refer to?

Lines 289-290: delete "A summary of the management practices observed over all pens can be seen in Figure 3."

Line 290: insert "(Figure 3)" after "99%"

Line 295: replace "that were all" with "tails"

Lines 298-299: delete "A breakdown of the category type and amount of enrichment observed in the pens is provided in Table 4."

Line 300: insert "(Table 4)" after "items"

Line 311: delete "Table 5 shows the level of risk assigned by the assessors with relation to each risk category"

Line 312: replace "minimum" with "minor"

Line 314: insert "(Table 5)" after "system"

Lines 315-316: delete "Table 6 reported the level of risk assigned for those pens where assessors reported no risk for tail biting."

Line 317: insert "(Table 6)" after "factors"

Table 5: please explain the percentages. Based on the title, values between 0 and 2 would be expected.

Line 326: change heading to "4.4 Skin damage"

Lines 327-330: Is the data presented somewhere in the manuscript?

Lines 334-337: Indicate the variation in the values that the statistics report. Reduce the 2 significant figures used in Line 335 to only 1 significant figures as in Line 337 for consistency.

Lines 338-339: If the data presented somewhere, please indicate. If not, please provide the values.

Line 350: Figure 5 only shows pig production stage, so remove "the amount of enrichment provision"

Line 353: more what?

Line 365: the data is not in Table 2

Line 375: indicate the association value

Lines 377-379: are Feeding System and feeding space confounded?

Lines 384-385: delete "Table 7 shows the number of lesions found by the assessors for each body condition listed in the risk

protocol, divided according to whether the risk of tail biting was detected."

Line 388: insert "(Table 7)" after "not"

Line 387: how was "no difference" determined?

Lines 397-398: Is the data presented somewhere in the manuscript?

Lines 417-546: were not carefully reviewed due to limitations in the results discussed previously

Figures 4-7. The standard error values seem very large and should be checked. All the values in the figures should be labeled to indicate statistical differences. Providing a single letter does not indicate which values are different from each other.

Reviewer #2: In their study, D’Alessio et al. Investigate the utility of a tail biting risk assessment tools for veterinarians. This tool includes a classification of several management and health xxx in combination with observations of behaviours to assess the risk of tail biting on farm. The risk assessment of trained veterinarians was compared to actual lesions recorded at the slaughterhouse and found to be not reliable. The authors provide a range of reasons why the tool failed in their article. Although the results provide a valuable overview of the prevalence of tail biting and reflect management practices in Ireland, they appear to be of limited interest to other countries with different assessment tools, particularly as the authors do not suggest any major improvements to the tool or training.

In general, the tool is insufficiently described. Without prior extended knowledge of the WebHat protocol, the protocol is difficult to understand. The authors should be clearer in explaining how the risk categories are assigned from the parameters evaluated. For each level of the parameter, it should be made clear how this impacts the assessment of risk, for example if there is only marginal enrichment how does this translate in assessment of risk value? Does marginal enrichment mean a risk of 4 in the category? What are the expectations regarding, for instance, vaccination status or mixing of sexes, and tail biting?

Throughout the results it is not enough to indicate (P<0.05) we need more information on the model output with information on the type of model, estimate, degrees of freedom, etc. This can be in the results section but also in a table. Same for the correlation outputs, just indicating rho values is not enough.

Material and methods

Line 119: The assigned values should be explained in the text and not only in the table. Please also give more details as to how the assessment was conducted for each category.

Table 1: “Risk 0: Risk not observed, Risk 1: Risk Category Statement is correct, Risk 2: I was not able to identify risks associated with this Risk Category, Risk 3: I have identified that risk exists for this Risk Category Risk 4: There are clearly risks associated with this Risk Category” this is very unclear and confusing and should be rephrased. I find this difficult to read and difficult to understand, I think adding in text explanations would help. For example, Risk 1 for the first category means “the risk category statement is correct” and the statement says “Environmental enrichment provision represents no risk for tail biting” so to me that means risk 1 there is no risk but risk 2 level says “I was not able to identify risks associated with this Risk Category” so risk 2 means there was no risk too? This is extremely confusing and need to be carefully explained. Putting values from 0 to 4 seems to hint that there is a hierarchical order but in that example I see no difference between risk 1 and 2.

Line 169: It is unclear to the reader what the sample size refers to, please clarify whether this is the number of animals per year or farm where you got permission for examination.

Line 212: consider using “grouped” instead of “collapsed”.

Line 213: there is one “and” too much in the parenthesis, consider replacing it with a comma

Line 220-221: Here, the associations between the risks and their indicators are presented; however in table 3 it is written “indicators hypothesised to be associated with each risk category” which is not specified in the text. I find this confusing as in the next line it says that only indicators associated with a risk factor were included in the analysis but it is unclear how these associations were decided and whether they are real or predicted.

Table 3: please provide information on how to interpret this table. It is not clear to me, for example, how dirty flanks are indicative of thermal comfort (or the lack of it).

Line 240 and 265: Please specify if the model was linear or generalized linear; in the latter case, which distribution was used.

Line 242: I assume these indicators were the response variable, but I feel this could be made clearer. To me it seems there was a separate model for each of these variables with management practices as fixed factors and pen as a random effect, is this accurate?

Line 245 and 246: factors instead of effects? I assume the number of pigs per drinker was also a fixed effect, but a continuous one.

Line 275: Tendency toward significance does not represent statistical significance and therefore should not be discussed as it can lead to over interpretation.

Line 277: The nature of the transformations needs to be specified for each variable they were necessary and for each model.

Results

Table 4: it is unclear what the categories mean, provide more detail in the text. For instance, is it the number or the type of enrichment objects that are classified as “suboptimal” etc.?

Line 308: What level of risk value does “considered to be a risk” refer to? It would be good to specify clearly if this is from risk 1, or 2. As I mentioned above, the risks levels are not well explained and make this difficult to understand. “assessors” instead of “assessor’s”.

Line 312: Please define in the methods what is the level of minimum risk. The risk category levels as explained in the methods are not clear enough to establish what is the minimum reported.

Table 5: Minor and Major risks need to be defined in the methods. From my example above I do not see how risk 1 is a minor risk from enrichment as risk 1 says the statement “Environmental enrichment provision represents no risk for tail biting” is correct. No risk for tail biting is not minor risk. Additionally, why are risk 3 and 4 not mentioned?

Table 6: does this table include the first row of Table 5? It is unclear what the table shows, and, in particular, what the difference is to Table 5.

Figures 4-6: difficult to interpret the letter, what are the comparisons? Why “P<0.05” in Fig. 7? There is no letter indicating statistically significant difference?

Line 368: provide p-value with coefficient

Discussion

The discussion is well written and I mostly agree with it. However, it is often mentioned that some observations and findings are contrary to the literature, because conditions prevented the assessors from measuring the variable correctly, or because insufficient training resulted in a lack of reporting of certain variables (such as injuries). In this case, however, this makes the evaluation rather unreliable, because if the assessors could not assess the different variables correctly, then it is difficult to draw any conclusions from this study.

It seems to me that the method was not standardized enough and allowed for too much interpretation by the assessors, which led to results that were ultimately uninformative.

Unfortunately, the discussion is confined to describing the situation and explaining the results, but do not suggest how to proceed or how to solve the problem, which would have made the manuscript of broader interest.

Reviewer #3: The paper is a very well written and understandable document that presents interesting data related to Evaluation of a tool to identify risks for tail biting in pigs, that fits the Scope of PLOS One.

In my perspective the study has some main limitations that should be improved by the authors:

- Please provide the assessment protocol (Supplementary material) and, more important, provide the typology of the answers to each evaluation made (e.g. qualitative, score, presence/absence....etc.)

- Line 93 “designed to take a maximum of 15 minutes to complete per pen by a trained assessor (S1).”- Please add how many pens need to be evaluated per farm (it is written after, but I think that it should be also add here)

- Line 98 - How the assessor obtained the final weight achieved in the pen?

- Line 100 101 : How the assessor considered the vaccination protocol to be appropriate? Plesae clarify

- Line 106: Evaluation of physical and behavioral welfare indicators. It is not clear how this evaluation was performed for each variable assessed (e.g. score for each injuries or presence/absence?). Please clarify.

- Line 116: “Estimate the level of risk of tail biting in relation to six risk categories.” This output it is extremely subjective. There was any score used to support the assessors? Please clarify

Line 120: “In each farm the assessor was asked to assess six pens; two at first stage weaner (from weaning day to approximately four weeks after weaning), two second stage weaner (from approximately four weeks after weaning to moving pigs to the finisher stage), and two finisher pens.” How the assessor selected the pens? The assessor evaluate the six pens in the same day? The risk estimated is a general risk per farm or per stage of production? The finisher pigs are the ones observed at abattoir? The pigs evaluated at the weaning stage are not the ones evaluated at abattoir? I’m asking this because the majority of tail biting outbreaks occurs at this stage and consequent severe tail loss with healing may be seen at abattoir. If these animals are not followed to the abattoir, some correlation analysis may failed. Please clarify these questions. Please explain the relationship between the batch of pigs sent to the abattoir with the assessed pigs at farm level

- Line 172 - Define representative sample

- Line 185 - Please define: severe tail loss with healing

- Figure 1: Photos from score 0, 1, 2 and 3 are not original. Please add the source

Line 486 - “ Our results indicate that the prevalence of pigs with the investigated injuries was low, and that visible injuries were not influenced by the production stage, or the number of enrichment materials provided per pen”. Please add some discussion regarding the fact that the majority were docked pigs which may have influenced the result you found. Please add the same information to the conclusions: Line 554 “ Limitations associated with the implementation of the tool include the relative inexperience of the assessors, and the challenge presented by recording animal indicators from outside of pens”

Line 520 - “The lack of association between the two again suggests that in its current deployment, the application of the tool was not effective at identifying risk in general, even without considering the six specific risk categories”. Please add some information/discussion about the possible bias if pigs with severe tail lesions at farm could have been euthanised or not included in the batch assessed at abattoir level.

Since Assessment of tail biting it is a topic of major importance in pork production chain, this submission may be suitable for publication, if authors improve the limitations aforementioned.

Reviewer #4: This study is very valuable because a significant reduction in the risk of tail biting can be achieved on many farms through the systematic evaluation and modification of management practices. The study aimed to validate a novel tail-biting risk assessment protocol by examining its association with tail lesion scores observed at slaughter. The authors indicated the inefficiency of the assessment tool in identifying actual risk, on farm. It underscored the need for enhanced training, and improvement at farm level in areas such as stocking density, enrichment provision and reducing tail docking, which are practical working solutions.

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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

Reviewer #3: No

Reviewer #4: No

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PONE-D-23-38802R1Evaluation of a tool to identify risks for tail biting in pigsPLOS ONE

Dear Dr. D'Alessio,

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.

==============================

ACADEMIC EDITOR: 

• The paper needs a minor revision.

==============================

Please submit your revised manuscript by May 18 2024 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,

Faham Khamesipour, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

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.

Additional Editor Comments:

The paper needs a minor revision.

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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 #1: All comments have been addressed

Reviewer #2: (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 #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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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 #1: Yes

Reviewer #2: 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 #1: Yes

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 #1: (No Response)

Reviewer #2: In the revised version, the authors provide more information and detail (esp. Supporting Information is valuable to understand the protocol), and the results are better documented. The conclusion has been much improved, with some suggestions how to improve the tool.

However, some of the author’s responses to reviewers’ comments raised eyebrows; it really underscores that the assessors were not properly trained and the results issued from the application of the tool are not standardized at all.

«It transpired that the assessors used the levels in a different way than instructed» Similarly, “Assessors were consulted, and they informed the authors that they considered both level one and 2 to imply that there was minimal risk for tail biting in the pen. Levels 3 and 4 were being applied interchangeably whenever a risk factor related to that risk category could be clearly identified”. Risk categories: “However these were inserted by an external party who was also involved in the development of the tool, without piloting the definitions with either potential assessors or other personnel involved in the tool development”

So assessors just decided upon themselves to use the levels interchangeably: these issues should have been reported by the assessors and the procedure adapted accordingly during the study.

It has to be made clear already in the abstract that the results have to be taken with a grain of salt, and that the tool lacks standardization and the assessors lack proper training. Readers should already know before they read the main text of the article that the authors tried to implement the tool but faced major issues and that they offer recommendations for those developing such tools in other countries. Knowing this beforehand avoids wasting readers’ time when they expect clear results.

“due to the poor performance of this risk assessment protocol, a second one was developed and now in phase of validation. The new risk assessment tool aims to be more specific, to help assessors (and farmers) to obtain a clear insight of weakness and strength of the farm.”

This raises the question if it would not have been better to wait for those results before publishing. There should be a clear benefit in publishing the failed tool for other researchers! Again, it should be highlighted in the abstract.

Overall, the results are still a bit difficult to understand and it is not clear what authors exactly want to show.

Table 7: I do not understand this table: if this is in a sample of pens where there was no risks then why is there a line with major risks.

Figure 6: in the method there are now 3 levels: 0 being when the risk was not observed, then low risk and high risk. Here I suggest changing 0 and 1 to low and high if that is what it refers to.

L 290: suggestion: random effect instead of repeated effect.

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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 #1: Yes: Ryan Samuel

Reviewer #2: No

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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.

PONE-D-23-38802R2Evaluation of a scheme to identify risks for tail biting in pigsPLOS ONE

Dear Dr. O'Driscoll,

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.

I would like to say that I think that the paper has improved and it is suitable for publication after some minor comments.

Please submit your revised manuscript by Jul 12 2024 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,

Faham Khamesipour, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

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.

Additional Editor Comments:

I would like to say that I think that the paper has improved and it is suitable for publication after some minor comments.

Comments for authors

Lines 256-260: methodological question. The risk on doing this pen level estimate is that some pigs had a high number of lesions. Do you have a measure of disperson (Standard error), or do you work with the median or some parameters which avoids not considering the variation in data? I am not sure if this is reflected in your results in Table 8, since the interquartile range you provide is already of pens not of individuals within a pen.

Another variable, ‘Visible injuries’ was created by summing the number of tail, ear, flank and aggression lesions in the pen, and dividing by the number of pigs per pen to provide a pen level estimate relative to the number of pigs

Line 291. It seems that pens were only observed once, why is it used as repeated effect?

Line 355. For the undocked pigs, it is understood that you used the same scoring system at the abattoir? Do you think you should use in futur studies a different one, which could evaluate lenght?

Lines 571-578. Take into account my previous comment on the fact that when you score at pen level injuries, one biased factor could be disperion (ie animals heavily injured increasing the overall score)

Line 614- 625. In my opinion, this problem about lack of correlation between on farm risk assessment and at abattoir final result could be worse in undocked pigs. Your sample size is probably not sufficient to separate both types of pigs, but it would be an interesting study for the study. Not only because tail biting is still more problemàtic in undocked pigs, but because the scoring system at the abattoir needs to be able to disentangle those pigs which has suffered tail biting but lesion has healed over time.

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Reviewers' comments:

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Reviewer #5: All comments have been addressed

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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 #5: Yes

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

Reviewer #5: Yes

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Reviewer #5: (No Response)

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Reviewer #5: Yes

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Reviewer #5: (No Response)

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Reviewer #5: Yes: Emma Fàbrega Romans

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Evaluation of a scheme to identify risks for tail biting in pigs

PONE-D-23-38802R3

Dear Dr. O'Driscoll,

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Additional Editor Comments (optional):

The comments the reviewers made have been addressed. I think this kind of practical information is very useful when published for researchers to know what happens in commercial settings and address future research topics.

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 #5: 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 #5: Yes

**********

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

Reviewer #5: 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 #5: 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 #5: 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 #5: Dear authors

Many thanks for considering my comments. The paper is now suitable for publication. Nice piece of work.

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Reviewer #5: Yes: Emma Fabrega Romans

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