PONE-D-21-23001Testing the locally-adaptive model of archaeological potential with hunter-gatherer sites in the Tanana River valley, AlaskaPLOS ONE

Dear Dr. Driver,

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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Dear authors,

Following two differing opinions from reviewers, and my own assessment of the manuscript submitted to PLOS One, I am recommending Acceptance of your submission subject to major revision.

Please find below detailed comments from both reviewers. As highlighted by R1, I found your approach with the improved modelling informative, particularly with regard to overcoming aspects of diversity in site location and landscape/environment related variables. Furthermore, I laud the efforts and approach of the authors in using and building on open source software. At the same time, as raised by R1, it would be good to state more explicitly how analysis scripts will be made available, and if the fully open access deposition of these is not possible (e.g., due to permit, government regulation, legal requirement, etc. related restrictions) please consider if protected deposit at a research data repository could be possible. In your revision, please ensure that all data sources, analysis components, scripts, and details of access to other sources of information are either included in supplementary materials and/or clearly linked to in existing data repositories.

Most importantly, Reviewer 2 has serious concerns regarding the reproducibility of the analyses presented. I am not convinced that a wider (i.e., by the commercial archaeology sector) lack of access to high-power computing facilities has a bearing on the reproducibility of this manuscript. At the same time, the responsibility falls on the authors to make explicit all the necessary hardware, software and datasets to ensure that this novel and important methodology can be applied as widely as possible. To this effect, please note that PLOS One is very generous on word count/space made available for major research articles, and most types of data/scripts can be easily included as supplementary materials. Should you have any further queries please do not hesitate to get in touch with myself or with the editorial office.

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We look forward to receiving your revised manuscript.

Kind regards,

Ceren Kabukcu, PhD

Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

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Reviewer #1: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: 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 LAMAP approach certainly overcomes some issues of predictive modelling and in particular focussing on variability of landscape parameters and not using non-site locations. Further more, an application to hunter-gatherers is a welcome addition to the previous papers on the topic.

Though, this is an excellent paper, the authors might want further improving it by addressing some points:

- In the introduction reasons for predictive modelling are mentioned. A well known problem is that this approach can enable us to find some sites and prevents us from finding other sites because the research focus bias. The other sites might be more telling. The better the prediction methods, the higher the bias. A sentence why this approach is nevertheless useful and valuable would be nice.

- It would be helpful to say something about the size of the surrounding of the sites in the method section. Later it is mentioned that the size is 1 km diameter circular quadrat (my English is not good enough to understand this term. How can a quadrat be circular? Four corners are a quite bad approximation of a circle), but this decision is not explained. A connection to site catchment approaches could make sense. Anyway, why this particular size?

- The PCA is another important issue. The benefits are explained but it remains open at which level the new variables are skipped and why ignoring this information would be appropriate? Since PCA is ordering the new variables according to variability, an overvaluation of large variability is inevitable. It should be explained how this concept is supported by the underlying theory of the LAMAP approach.

- Finally, the analysis uses open source software which is very good. But is the analysis reproducible? The data will fully available but are the analysis scripts also available? (It might be mentioned that the reviewer does not consider "accessible to qualified researchers" as fully available and does not belief that "protect sites from vandalism" is an appropriate reason but that need not be the subject of this report, as this is not always a decision of the authors.

Feel free to contact me if you have any questions.

Oliver Nakoinz

Reviewer #2: Summary

This paper employs an off-the-shelf, but relatively new, method for generating statistical predictive models for archaeological site locations and does so to evaluate its efficacy for use by hunter-gatherer archaeologists. It is cleanly written and well organized, although the latter could be improved a touch to strengthen the manuscript. I also found the methodology appropriate and results supported by the data. The conclusions make sense too. While a generally sound paper, given that it neither presents a novel method nor evaluates a well-developed archaeological question, I feel it a better candidate for a regional journal. I also have issues with replicability that I suggest the authors consider and these are discussed below.

Comments

1. Would like to see the hypothesis in play stated explicitly along with the predictions under test.

2. This paper seems of two minds. I found it unclear if this is an evaluation of the methodology or the exploration of an archaeological question. I would pick one and concentrate on making the relevant point. Because this in not a test of a novel methodology, I might focus instead on using it to answer a well developed and (at least) regionally important research question about settlement patterns in the Tanana River Valley. As is, we get, did site locations change through time? as the research question, but why this is an important question is never discussed in any meaningful way.

3. While I think that points one and two can be easily addressed, I do have issues with the replicability of this study and this is one of the important publication criteria for PLOS. The primary issue here is that very few of us have access to national laboratory level main frame computing clusters. My concerns here are twofold. First is the observation that to replicate this study one needs access to similar computing power. This limits replicative studies to only those with similar computing capabilities and renders this method an “insiders” approach. Second, this study appears aimed at cultural resource management archaeologists, the vast majority of which are working on Best Buy quality and performance-level laptop or desktop computers. To me, this is a substantial and important disconnect between the study and suggested real-world application – I can‘t ready replicate the study, nor can I (or the vast majority of archaeologists, especially those in the target audience) employ the methodology for my own research.

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Reviewer #2: No

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Does the Locally-Adaptive Model of Archaeological Potential (LAMAP) work for hunter-gatherer sites? A test using data from

the Tanana Valley, Alaska

PONE-D-21-23001R1

Dear Dr. Driver,

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.

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Kind regards,

Ceren Kabukcu, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: