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π @takayabe0505 @ssujit @jlevente This is the review thread for the paper. All of our communications will happen here from now on.
Please read the "Reviewer instructions & questions" in the first comment above.
Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5201 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.
Software report:
github.com/AlDanial/cloc v 1.88 T=1.54 s (27.8 files/s, 20969.9 lines/s)
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Language files blank comment code
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Jupyter Notebook 11 0 20418 3844
Python 10 849 2334 2972
XML 9 0 0 1401
Markdown 4 61 0 187
reStructuredText 4 84 54 84
YAML 2 5 11 29
TeX 1 0 0 24
make 1 4 7 9
TOML 1 0 0 6
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SUM: 43 1003 22824 8556
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 728
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- None
MISSING DOIs
- None
INVALID DOIs
- None
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
:wave: @ssujit, @jlevente could you give me a short update as to how things are going with your reviews? Thanks!
:mega: Mid-week Rally! :mega:
@ssujit and @jlevente could you give me a short update as to how things are going with your reviews?
Thanks!
:wave: @ssujit and @jlevente could you give me a short update as to how things are going with your reviews?
@ssujit let me know if you are having trouble creating your reviewer checklist.
Please update π ...
π @ssujit and @jlevente could you give me a short update as to how things are going with your reviews?
@ssujit let me know if you are having trouble creating your reviewer checklist.
π¨ MIDWEEK RALLY π¨
@ssujit and @jlevente - Could you please provide an update to how things are going here? Please do let me know if you are unable to review this article so I may move it forward. As always, let me know if you have any questions!
Have a great day!
β Last call for a response before I have to assign different reviewers @ssujit and @jlevente! Please respond in this thread if you are able to conduct this review within the very near future. Thanks!
@takayabe0505 I am removing your current reviewers due to no response. I will find you two more to keep this review going. Apologies.
@editorialbot remove @ssujit as reviewer
@ssujit removed from the reviewers list!
@editorialbot remove @jlevente as reviewer
@jlevente removed from the reviewers list!
:wave: @ifthompson can you help out with this one?
:wave: @levisweetbreu let me know if you are able to help out with this one. Thanks!
@crvernon Yes, I can review this in the near future.
@editorialbot assign @ifthompson as reviewer
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@crvernon I would be happy to help out!
@editorialbot add @levisweetbreu as reviewer
@levisweetbreu added to the reviewers list!
π @ifthompson and @levisweetbreu
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 @ifthompson & @levisweetbreu , 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 me know.
@ifthompson and @levisweetbreu
This is the review thread for the paper. All of our communications will happen here from now on.
As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.
The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5201 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.
We aim for the review process to be completed within about 3-4 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.
π @ifthompson and @levisweetbreu how are we doing on this submission? Are there any other outstanding issues?
:wave: @takayabe0505 - I see there are a few outstanding issues. Do you know when these will be resolved so that we can move forward? Thanks!
@crvernon those issues have been left open by me, there are two outstanding concerns I have.
The first is probably semantic, but the checklist asks if the submitting author has made major contributions to the software. I am confident that significant scholarly work has gone into this software, but the only work I can see in the commit history is from @ubi15 (who is the lead author on the paper), not from the submitting author @takayabe0505. I wanted to know your opinion on this before moving forward.
The second concern is with the proprietary dataset mentioned in the paper and used in the software tutorial. Although the author's don't make specific claims or results in the paper, the project they mention does not have open-source data and thus cannot be replicated. The authors do supply some open-source data in the tutorial, but it is difficult to verify the functionality of the software when most of the data used is proprietary, especially because the software does not use automated tests.
@crvernon those are the only items I wanted to check with you and see JOSS's opinion on, otherwise I am comfortable giving the OK on this submission.
@crvernon aside from what @levisweetbreu has mentioned, I think the community guidelines just need to explicitly mention that users are welcome to raise an issue to 2) Report issues or problems with the software 3) Seek support
, as per the review checklist, not just to contribute. @takayabe0505 let me know if I have missed this somewhere in the documentation, otherwise it should be a quick add to the README.
Not a blocking issue, but non-specialists reading the paper might benefit from the term "mobility data" being defined early on. I think from context it's clear enough to understand, but for those outside of this field, "mobility" can be more associated with as the ability to physically move (e.g., move your body's joints), rather than high frequency location data.
@crvernon One last thing: JOSS's Human participants research policy primarily relates to medical data, rather than privacy/ethics concerns with this kind of location data, such as determining home/work location. The documentation mentions that mobility data often has noise added near the user's home in order to preserve their privacy, so home location cannot be determined with higher resolution than this noise if present, but does JOSS have any guidelines relating to software that works with this kind of data?
Once these are addressed I think this is good.
@levisweetbreu Hello, regarding the contribution from my side, I was the author of the first version of most of the functions that were implemented as part of the work for the World Bank. @ubi15 then cleaned the code and formatted them into production level code, and then committed to the github repo. I believe this is sufficient as a significant contribution on the software.
@ifthompson We have addressed the following comment
One comment is: I think the community guidelines just need to explicitly mention that users are welcome to raise an issue to 2) Report issues or problems with the software 3) Seek support, as per the review checklist, not just to contribute. @takayabe0505 let me know if I have missed this somewhere in the documentation, otherwise it should be a quick add to the README.
Please see the 7b50b0e commit, thanks!
π @takayabe0505 @ifthompson and @levisweetbreu
Could you provide an update in this thread to how things are going and what is left to complete for this review? Thanks!
@crvernon I need input from you on the issues I mentioned in my previous comment, namely the authors' use of proprietary data in the paper and for verification of the software.
:wave: @crvernon β I think the author is seeking your feedback here.
Thank you! I'll reply in full here later today. I am on business travel but will have time tonight.
@levisweetbreu ... to address your questions:
Question 1:
The first is probably semantic, but the checklist asks if the submitting author has made major contributions to the software. I am confident that significant scholarly work has gone into this software, but the only work I can see in the commit history is from @ubi15 (who is the lead author on the paper), not from the submitting author @takayabe0505. I wanted to know your opinion on this before moving forward.
I believe the response from the author is sufficient to meet this requirement. See:
@levisweetbreu Hello, regarding the contribution from my side, I was the author of the first version of most of the functions that were implemented as part of the work for the World Bank. @ubi15 then cleaned the code and formatted them into production level code, and then committed to the github repo. I believe this is sufficient as a significant contribution on the software.
Question 2:
The second concern is with the proprietary dataset mentioned in the paper and used in the software tutorial. Although the author's don't make specific claims or results in the paper, the project they mention does not have open-source data and thus cannot be replicated. The authors do supply some open-source data in the tutorial, but it is difficult to verify the functionality of the software when most of the data used is proprietary, especially because the software does not use automated tests.
I think this is a valid concern. Though the requirement is that the software provided be open-source, the need to actually ensure that it is working as claimed is a part of this review. @takayabe0505 is there a way to ensure the functionality claims of this software without the use of proprietary data?
@takayabe0505 just coming back the the question above β¬οΈ
@takayabe0505 following up again on the aforementioned. Let me know if you have any questions! Thanks!
Hi @crvernon sorry for the late response. We used open source data (there's only 1 publicly available open dataset we know of - the GeoLife data; https://www.microsoft.com/en-us/research/publication/geolife-gps-trajectory-dataset-user-guide/) to make sure our functions work properly, in the 'Quickstart' section in the documentation: https://mobilkit.readthedocs.io/en/latest/examples/mobilkit_tutorial.html#
I hope this satisfies the reviewers' concerns. Thanks!
@levisweetbreu note:
Hi @crvernon sorry for the late response. We used open source data (there's only 1 publicly available open dataset we know of - the GeoLife data; https://www.microsoft.com/en-us/research/publication/geolife-gps-trajectory-dataset-user-guide/) to make sure our functions work properly, in the 'Quickstart' section in the documentation: https://mobilkit.readthedocs.io/en/latest/examples/mobilkit_tutorial.html# I hope this satisfies the reviewers' concerns. Thanks!
@crvernon If this meets the JOSS requirements, then my concerns are satisfied, and I approve this submission for publication.
@ifthompson are we all good from your side of things?
@takayabe0505 there are still two open issues related to this thread:
https://github.com/mindearth/mobilkit/issues/5
https://github.com/mindearth/mobilkit/issues/6
Have these been satisfied?
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:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @crvernon know.
β¨ 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 β¨
Checklists
π Checklist for @levisweetbreu
π Checklist for @ifthompson