Dear Dr. Meijaard,

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Edvard Mizsei

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?

Reviewer #1: No

Reviewer #2: Yes

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

Reviewer #1: No

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: No

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4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: The study tackles an important conservation question: how far citizen science observations can inform species occupancy in human-modified tropical landscapes. The effort to compile and analyse such a large dataset is commendable, and the manuscript is generally well written.

However, I do not consider the current analysis to provide reliable or actionable ecological conclusions.

Detection probability and data quality:

Many species show very low detection probabilities (<0.1), resulting in wide confidence intervals and highly uncertain occupancy estimates. Such limitations cannot be addressed by simple manuscript revisions; they would require different data collection strategies (standardised sampling).

Model fit and spatial limitations:

The lack of precise site level coordinates (especially within HCV areas) further constrained the use of spatially explicit models. These shortcomings compromise the validity of the inferred habitat relationships.

Restricted species set:

Although over 300 species were recorded, occupancy analysis was workable for only 23 of them. This narrow focus reduces the generality of the conclusions for biodiversity management.

Interpretation of results:

The manuscript sometimes overstates the practical management implications of the findings. The data currently highlight the challenges of using opportunistic observations rather than delivering strong conservation guidance.

Presentation:

The writing is clear.

I therefore recommend rejection of the manuscript in its present form.

Reviewer #2: The objective of the MS is to explore novel methods of using N-mixture models to estimate occupancy by wildlife in particular habitats, using unstructured data obtained from citizen science surveys/occasional observations. With the increasing role of citizen science data collection in biodiversity sciences, this study is particularly important to explore how these unstructured data can be exploited to better understand the reaction of wildlife to alterations of natural habitats into landscapes serving human needs. In particular, the MS intends to overcome the problem of missing non-detection records. This manuscript is highly relevant in light of the quickly accumulating unstructured biodiversity data globally: via mobile applications (iNaturalist and others), data liberation from past and current publications via machine reading, from museum collections, data accumulating in data aggregators (i.e. GBIF etc.). The analyses of these data will require new and refined methods such as the one presented in this MS.

I consider this MS suitable for publication in PLOS ONE with a minor revision.

Language: As a non-native English speaker, I, in general, find the language clear and easy to understand. However, in some parts, the text would benefit from further polishing by a native speaker.

Remark on the Introduction and Discussion

The authors’ scope of the usefulness of their study, in my opinion, is a bit narrow. Their approach and methods are applicable in a wider scope (see my introductory overview). I recommend reviewing the literature shortly to include other fields of application in addition to what they indicated. The published paper would greatly benefit from opening up the scope of applicability (at least at the level of mentioning with a few references): historical miscellaneous data extracted from past literature, national park data repositories, data from museum specimens or biodiversity data aggregators etc.

Tables and figures:

Table 4: It would be helpful for the reader to group the observed taxa into higher taxonomic groups: Reptilie/Reptiles, Aves/Birds, Mammalia/Mammals and indicate the category in a subheading above each group. Maybe even at the level of order it would be reasonable to group them, e.g. not to mix primates with rodents. Also in S2.

In the legends and headings of tables 1,2. the names of the variables should be self-explanatory and given in a standard way: Nsites = No. of sites, etc. Also symbols or words should be standardised across the table legends/headings: either /(slash) or per.

Fig 3A-B, scientific names should be Italicised.

Minor issues:

Line78: References outside the sentence!

Line83: Instead of intensively studied it would be better to say intensively surveyed or sampled.

Lines118-119: “Some sites which were never surveyed;” “which” is not needed.

Lines 135-138: I have no deep understanding of the model, but this sentence seems to me in any case vague. It should be clearer for the benefit of the lay readers.

Line266: Varanus as a generic should be abbreviated: V. as it is the second mention in the MS. See also Pongo in Line280. See also guidelines of PLOS ONE.

Line286, Parenthesis after dove species should be deleted.

Line293: Consider rewording into: Often but not always in the alternative dataset, the same model was selected as top model as in the standard set.

Lines298, 303 and 305: data should be dataset.

Line309: Consider sentence revision: Many researchers pointed out the downsides of the collection and analysis of unstructured data:

Remark: The authors indicated that they have not have yet the full consent from the data owners to make the raw data available. Whatever the final decision will be the MS is still worth publishing.

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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

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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.

Occupancy estimation of wild species in a palm oil plantation using unstructured data

PONE-D-25-36925R1

Dear Dr. Meijaard,

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.

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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,

Edvard Mizsei

Academic Editor

PLOS One

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions??>

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

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #2: Yes

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Reviewer #2: I found the topic and the promising method valuable. Even if the data has shortcomings what the authors admit, the methods explored here are promising, especially in light of the increasingly available unorganised data (citizen science, data liberation from literature, museum specimens). I hope that the authors will have the opportunity to further develop their methods.

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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

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