PONE-D-21-10041

Change of human mobility during COVID-19: A United States case study

PLOS ONE

Dear Dr. Anderson,

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.

The attached review is comprehensive, please make edits in respond to each reviewer's remark

  

Please submit your revised manuscript by May 27 2021 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: http://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,

Itzhak Benenson, 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

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. Thank you for stating the following in the Acknowledgments Section of your manuscript:

This research is supported by National Science Foundation “RAPID: An Ensemble Approach to Combine Predictions from COVID-19 Simulations” grant DEB-2030685.We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form.

Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows:

T.A. A.Z. H.K.

Award no: 2030685

Funder: National Science Foundation

Funder website: nsf.gov

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Please include your amended statements within your cover letter; we will change the online submission form on your behalf.

3. We note that Figures 5, 6, 7, 9, 10 in your submission contain map images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission:

3a, You may seek permission from the original copyright holder of Figures 5, 6, 7, 9, 10 to publish the content specifically under the CC BY 4.0 license. 

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

3b, If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

4. 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

**********

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

Reviewer #1: 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

**********

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

**********

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 is a well-constructed and useful paper. The authors present a robust methodology, which is essentially a large scale clustering project, and with which I have no quibbles. My comments pertain more to reconciliation of data science vs. epidemiology terminology, and the need to further caveat the data sources.

Abstract: "Mobility in 2020 for US counties can be explained as a combination of three trends"

It might be helpful to state these in the abstract.

Table 1: This is excellent and useful. I have made a nearly identical table in my own research, so glad to see this find its way into print.

Methods section 2: "Delta Measure of Public Exposure"

This is semantic: I understand the meaning of this within this context. However, as an epidemiologist, the term "exposure" has a more specific meaning, which is not adequately represented by gross mobility measures. Within epidemiology, "exposure" means direct exposure to the causative agent. Mobility is a proxy for that. The authors may consider modifying the term to avoid detracting from what it otherwise and excellent paper. Similarly, in the discussion "Long term exposure reduction" will likely raise the hackles of public health audiences. Consider "Long term mobility restriction" as a more accurate representation of what was measured.

Discussion: While the data providers have gone to unprecedented lengths to make these data public during the pandemic, as the authors note, the descriptions of methods are sparse. In addition, there are few safeguards that the data will continue to be available, or any real measures of completeness. As such, more in the discussion is warranted about the potential limitations scientific reliance on corporate free data.

2.2 "We note that this measure only includes public POIs that are captured among the 6.5 million POIs in the SafeGraph Core Places database."

This is a perfect example of my previous point. We have no idea how dynamic or complete these POI are. Granted SafeGraph has a more transparent and vibrant community of practice than most of the other providers. But still, the reliance on proprietary data has limitations that could be more clearly addressed.

Methods: Please describe geographic missingness in the dataset, e.g., arising from fewer POI or lower cell trace volume, or measurement uncertainty. What percent of US counties are covered?

"To reduce the dimensionality of R we truncate the SVD to obtain only the first K dimensions "

Please define kappa a little better to give a real world sense of the truncation.

"SVD assumes that the ∆MoPE is derived from the sum of latent (individual) mobility changes."

Is it sum or averaged? The mobility measures usually report mean changes, so there is an additional assumption there.

Methods: How are the 3 latent PCs measured/differentiated in the aggregate mobility data? For example, how are health professionals identified?

Methods: Can you provide more information on SafeGraph "footfall" metric? Does this correspond more in urban areas where foot traffic is more common?

Methods: "it was discovered that the only neighboring county to Fairfax City in Fairfax County,"

Virginia is an annoying case in county-city geography, in my experience. Were both city and county designations used?

Methods: "Pearson’s R coefficient "

This is a measure of linear association. Is there any a priori reason to believe the relationship to be linear?

Methods: "variety of explanatory variables, including income, political leaning, employment, and COVID-19 cases and deaths for each county "

Is this the complete list of variables? COVID cases and deaths were not consistently reported during the study period. For example, were antibody and rapid test positives included? Was repeat testing for the same individual accounted for? Despite being widely reported in data science and news media, the epidemiologic veracity of case counts is highly questionable. This should be caveated accordingly. Other journals have refused to publish results based solely on these numbers.

Figure 3 vs. 4 -- Suggest a different color scheme between graphs because causal readers may confuse the two legends since the lines are so similar.

Figure 6: I do not understand the color wheel and the colored lines extended from it?

I am curious why baseline commute times/distances, weather, and stay-at-home orders were not considered as explanatory variables?

The figure resolution and map projection was of low quality in the review PDF. I assume this will be corrected in the final version.

**********

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: Yes: Nabarun Dasgupta

[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-21-10041R1

Change of human mobility during COVID-19: A United States case study

PLOS ONE

Dear Dr. Anderson,

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: Reviewer #2 raises important methodological remarks, please react to these remarks.

Please submit your revised manuscript by Oct 03 2021 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: http://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,

Itzhak Benenson, Ph.D.

Academic Editor

PLOS ONE

[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 #1: All comments have been addressed

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 #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: No

**********

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

**********

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: The edits and revision look good. Thanks for the attention to detail! The changes, both semantic and substantive are adequate. This is a nice paper. I look forward to being able to cite it.

Reviewer #2: I have read the manuscript “Change of human mobility during COVID-19: A United States case study”. The manuscript suggest a novel approach to identify the changes in human mobility between the years 2019 and 2020, using SafeGraph measure of median non home dwell time for each US county. The authors estimate the daily change in the measure between 2019 and 2020 in each county, find the principal components that explain most of the variance in the received time series, cluster the different county according to their principal components, conduct a spatial autocorrelation analysis between the counties, and a general correlation analysis of socio-demographic variables. The manuscript is concise, clear, and presents a solid framework for analyzing the change in mobility across the US due to the COVID-19 pandemic. However, the manuscript includes major pitfalls that should be addressed to in order to be published.

I divide my comments into general comments and specific comments.

General

1. In figure 2, it seems that TSPP in the summer of 2019 is lower than TSPP in January 2020. Although the authors do relate to the issue of the seasonal anomalies in the winters of both years, it seems highly unlikely that TSPP is higher in January of 2020 than in the summer of 2019. I suggest the authors run another check over the calculation to observe any mistakes. However, if no mistakes are found, I suggest the authors provide accurate data regarding the weather in each county and show that the weather in each county was indeed extreme. Since county s are not equal in size, a bias towards more dense areas exists, and extreme weather conditions in one of the metropolitan areas can affect the results. However, due to the fact that no data from previous years exist, and 2019 is presumed to be a baseline year, it is crucial to validate the weather conditions(for example, by using NOAA’s GHCN data) against the TSPP in order to explain the anomalies in TSPP.

2. Regarding the principle components analysis – what led the decision to choose only 3 PCs? It is important to show the distribution of the contribution of the PCs to the variability, and then explain what led to the decision to choose only the first three.

3. The choice of k = 3 in k means clustering cannot be explained using the 3 significant PCs. I suggest the author find a better explanation for using k =3, such as the k means bend method or other methods that exist for hierarchical clustering.

Specific

1. In definition 1, j should run between -3 and 3, in order to should that the moving average is of the middle day of the 7 day average

2. In definition 2, it should be noted that delta-TSPP is a by county measure, and therefore it should be parametrized and indexed as well.

3. In figure 2, an error bar/boxplot should be added for each day, in order to get a sense of the distribution of TSPP in the different counties.

4. 2.5 page 6: what state is Fairfax county?

5. Figure 6 is unreadable. I would remove it from the paper as it confuses the reader, and it is somewhat redundant given figure 5.

6. I suggest adding the share of population over 60 as one of the correlation analysis socio-demographic variables – it can help explain the positive coefficient of deaths per thousand in PC1, which is counterintuitive.

**********

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: Nabarun Dasgupta, MPH, PhD

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.

Change of human mobility during COVID-19: A United States case study

PONE-D-21-10041R2

Dear Dr. Anderson,

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,

Itzhak Benenson, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: