[REVIEW]: Mobilkit: A Python Toolkit for Urban Resilience and Disaster Risk Management Analytics using High Frequency Human Mobility Data

[editorialbot]

Submitting author: !--author-handle-->@takayabe0505<!--end-author-handle-- (Takahiro Yabe) Repository: https://github.com/mindearth/mobilkit Branch with paper.md (empty if default branch): Version: v0.2.8 Editor: !--editor-->@crvernon<!--end-editor-- Reviewers: @ifthompson, @levisweetbreu Archive: 10.6084/m9.figshare.24707115

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ssujit & @jlevente, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @crvernon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @levisweetbreu

📝 Checklist for @ifthompson

[levisweetbreu]

@crvernon I left those issues open in regards to my two concerns, so I just resolved them.

[crvernon]

Thanks @levisweetbreu !

[takayabe0505]

Thank you @levisweetbreu @crvernon !

[crvernon]

@ifthompson just following up ... are we all good from your side of things?

[crvernon]

After reviewing responses from @ifthompson, I believe we are good to move forward with my portion of the review.

[crvernon]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[crvernon]

:wave: @takayabe0505 Your paper and repo looks good from my side of things!

We are almost there! Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

• [x] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

• [x] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

• [x] Please list the DOI of the archived version here

I can then move forward with accepting the submission.

[crvernon]

:wave: @takayabe0505 - just following up on the above 👆

[takayabe0505]

Hi @crvernon , yes please give us a couple of days to figure it out! thanks :)

[ubi15]

Hi @crvernon , we published the zip and tar archives of the reviewed code here.

The DOI is 10.6084/m9.figshare.24707115

Please let us know should you need any other information and thanks again for your time and help!

[crvernon]

@editorialbot set 10.6084/m9.figshare.24707115 as archive

[editorialbot]

Done! archive is now 10.6084/m9.figshare.24707115

[crvernon]

@editorialbot set v0.2.7 as version

[editorialbot]

Done! version is now v0.2.7

[crvernon]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[crvernon]

Some final requests to your paper on per my last re-read:

• [ ] LINES 18-20. Should be rephrased, "While several tookits allow users to perform some basic analytics on large mobility datasets (e.g., De Montjoye et al., 2016; Pappalardo et al., 2019), these cover only some of the steps in the mobility data pipeline."
• [ ] LINES 21-22. Rephrase the following "Very often users have to go fishing for functions/tools from other libraries to cover for data pre-processing or visualization." to "These toolkits also do not provide adequate data pre-processing and visualization functionality which causes users to seek additional external options."
• [ ] LINE 23. Change "...documentation that enables..." to "...documentation to enable..."
• [ ] LINE 34. Change "...Notebooks that provides..." to "...notebooks that provide..."
• [ ] LINES 40-48. Create a new section titled "Use Case" to hold this content. Here is a revised version of these lines that reads more clearly: "The usefulness of Mobilkit was demonstrated in a recent study carried out in collaboration with the World Bank Global Facility for Disaster Reduction and Recovery. The study focused on assessing the impact of a 7.1 magnitude earthquake that occurred on September 19, 2017 where the epicenter was located around 55 km south of Puebla, Mexico (about 100 km south-east of Mexico City, Mexico). Mobilkit was used to conduct an analysis of the spatial structure of ten surrounding cities from smartphone location data, provided by Quadrant, which was collected before and after the earthquake to generate insights about management options. Similar analysis could also be explored using Mobilkit for planning and recovering activities related to climate, man-made, and other natural disasters." Please review my revisions in the above paragraph for accuracy

Once you have made these changes we can move forward. You do not have to conduct an additional code release or create any new DOI. Just alter the paper on your current, up-to-date branch that is being used in this review.

Thanks!

[ubi15]

Dear Chris, Thanks a lot for your review, we inserted all the changes in the paper as requested.

Below, you will find a report of the edits we performed as well as of the amendments applied to your suggestions.

We already pushed the commits to the main branch (commits 96761c and 936eca).

Feel free to write to us should you need any other edits or information.

Thanks! Enrico on behalf of the team

---

Edits

• [x] LINES 18-20. No edits, inserted as requested.
• [x] LINES 21-22. No edits, inserted as requested.
• [x] LINE 23. No edits, inserted as requested.
• [x] LINE 34. No edits, inserted as requested.
• [x] LINES 40-48. Some edits: we created the new section titled "Use Case" and changed the content to reflect the fact that we are referring to two separate works: one concerning the Puebla earthquake study -that we also added to the references- and the other dealing with Urban Spatial Structure -covering ten cities around the world. We added a footnote pointing readers to the Notebooks covering the latter topic as well. We are reporting here the revised version of the lines you suggested:

The usefulness of Mobilkit was demonstrated in a recent study carried out in collaboration with the World Bank Global Facility for Disaster Reduction and Recovery[@yabe2021location]. The study focused on assessing the impact of a 7.1 magnitude earthquake that occurred on September 19, 2017 where the epicenter was located around 55 km south of Puebla, Mexico (about 100 km south-east of Mexico City, Mexico). Mobilkit was also leveraged to conduct an analysis of the spatial structure of ten cities around the globe using smartphone location data, provided by Quadrant, to generate insights about mobility management options[^1]. Similar analysis could also be explored using Mobilkit for planning and recovering activities related to climate, man-made, and other natural disasters. [^1] See the notebooks covering Urban Spatial Structure analyses and an inter-city comparison of Urban Spatial Structure indicators.

And here is the bibtex of the added reference:

@misc{yabe2021location,
      title={Location Data Reveals Disproportionate Disaster Impact Amongst the Poor: A Case Study of the 2017 Puebla Earthquake Using Mobilkit}, 
      author={Takahiro Yabe and Nicholas K W Jones and Nancy Lozano-Gracia and Maham Faisal Khan and Satish V. Ukkusuri and Samuel Fraiberger and Aleister Montfort},
      year={2021},
      eprint={2107.13590},
      archivePrefix={arXiv},
      primaryClass={physics.soc-ph}
}

[crvernon]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[ubi15]

Hi @crvernon, thanks for the proof!

We actually discovered an error in my affiliation (I had a double one instead of a single one).

We already pushed the fix to our main branch, feel free to publish it then and sorry for the inconvenience.

[crvernon]

Thank you! I'll run my pass in the next few days.

[crvernon]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[crvernon]

Thanks for making the changes @ubi15 though we still have one more minor thing to fix in the paper before moving on to the next steps...

• [x] LINE 47: You are generating a footnote but it is not rendering correctly. Please ensure that 1) in the text that there is not space between options and [^1] which I believe you have accounted for; and 2) the footnote itself has the colon after it (e.g., [^1]: See the notebook...).

Here is an generic example:

Articles are published under a Creative Commons license[^1].
Software should use an OSI-approved license.

[^1]: An open license that allows reuse.

Thanks and let me know when you have this fixed up!

[crvernon]

:wave: @ubi15

I will be unavailable from Jan. 17-29. Please keep up the great work while I am out and I will be happy to address any questions you have when I come back!

Thanks!

[ubi15]

Hi @crvernon We implemented the changes, feel free to reach us back if anything is needed when you'll be back.

Thanks!

[crvernon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[crvernon]

👋 @ubi15 - we are almost there! Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

• [x] Conduct a GitHub release of the current reviewed version of the software and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

• [x] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

• [x] Please respond with the DOI of the archived version here

I can then move forward with accepting the submission.

[crvernon]

:wave: @ubi15 - just following up on the above requests. Let me know if you have any questions. Have a great day!

[ubi15]

Hi @crvernon - we published the updated code here and the corresponding DOI is 10.6084/m9.figshare.24707115.

Thanks again for all your help and support on this!

[crvernon]

@editorialbot check references

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[crvernon]

@editorialbot set 10.6084/m9.figshare.24707115 as archive

[editorialbot]

Done! archive is now 10.6084/m9.figshare.24707115

[crvernon]

@editorialbot set v0.2.8 as version

[editorialbot]

Done! version is now v0.2.8

[crvernon]

👋 - @ubi15 I am recommending that this submission be accepted for publication. An EiC will review shortly and if all goes well this will go live soon! Thanks to @ifthompson and @levisweetbreu for a timely and constructive review!