[REVIEW]: SVInsight: A Python Package for Calculating Social Vulnerability Indices

[editorialbot]

Submitting author: @mdp0023 (Matthew Preisser)
Repository: https://github.com/mdp0023/SVInsight
Branch with paper.md (empty if default branch): main
Version: v1.1.0
Editor: @sappelhoff
Reviewers: @dataspider, @bkrayfield
Archive: Pending

Status

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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

@dataspider & @bkrayfield, 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 @sappelhoff 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 @dataspider

📝 Checklist for @bkrayfield

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.22 s (647.2 files/s, 349434.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                             77              0              0          64839
HTML                            16            590             13           5220
CSS                              8            252             75           1512
Python                           7            417            847           1103
JavaScript                       7            131            197            817
YAML                             6             10              8            352
reStructuredText                13            312            136            321
TeX                              1             16              0            205
Markdown                         3             48              0             93
DOS Batch                        1              8              1             26
TOML                             1              3              1             22
SVG                              2              0              0             18
Jupyter Notebook                 1              0            117             17
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           144           1791           1402          74554
-------------------------------------------------------------------------------

Commit count by author:

   159	mdp0023
     7	Matthew Preisser
     1	Paola Passalacqua

[editorialbot]

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

✅ OK DOIs

- 10.2202/1547-7355.1732 is OK
- 10.1016/j.gloenvcha.2006.03.008 is OK
- 10.1016/j.ijdrr.2016.09.006 is OK
- 10.1111/1540-6237.8402002 is OK
- 10.2202/1547-7355.1792 is OK
- 10.2307/2137795 is OK
- 10.1111/risa.12677 is OK
- 10.3390/su12156006 is OK
- 10.1080/00045608.2012.700616 is OK
- 10.1016/j.apgeog.2015.06.011 is OK
- 10.5194/hess-26-3941-2022 is OK
- 10.3389/frwa.2023.1278205 is OK
- 10.1016/j.ijdrr.2021.102613 is OK
- 10.1080/24694452.2018.1535887 is OK
- 10.1007/s11069-019-03820-z is OK
- 10.1007/s11069-020-04470-2 is OK
- 10.13140/RG.2.2.35146.80324 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1231

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[sappelhoff]

Hello again! 👋


@dataspider, @bkrayfield

FYI @mdp0023

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).

✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.

💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link to #7212 so that a link is created to this thread. That will also help me to keep track!

❓ Please also feel free to comment and ask questions on this thread if you are unsure about something!

🎯 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.

[dataspider]

Review checklist for @dataspider

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/mdp0023/SVInsight?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mdp0023) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[sappelhoff]

Hey @bkrayfield 👋 could you please update us with an approximate schedule of when you intend to start and finish the review for this project?

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[bkrayfield]

@sappelhoff Sorry, work has me slowed down this time of year. Giving myself a deadline of Nov 11th? What the intention of finishing earlier.

[bkrayfield]

Review checklist for @bkrayfield

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/mdp0023/SVInsight?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@mdp0023) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[sappelhoff]

Sounds good to me @bkrayfield - thanks for the transparency.

[mdp0023]

@editorialbot commands

[editorialbot]

Hello @mdp0023, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[mdp0023]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf.

[mdp0023]

@editorialbot set v1.2 as version

[editorialbot]

I'm sorry @mdp0023, I'm afraid I can't do that. That's something only editors are allowed to do.

[mdp0023]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[mdp0023]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[mdp0023]

Thank you to the reviewers for their comments so far, I believe I have addressed them all so far in the latest version of the package (V1.2). I am happy to provide additional information or address additional comments as necessary.

[sappelhoff]

Thank you to the reviewers for their comments so far, I believe I have addressed them all so far in the latest version of the package (V1.2). I am happy to provide additional information or address additional comments as necessary.

Thanks for the update @mdp0023!

@bkrayfield @dataspider -- could you please update us with a tentative timeline of when you plan to finalize your reviews?

[mdp0023]

Hi everyone, just circling back to see if there are any other comments or questions I can respond to concerning the package or the paper.

[sappelhoff]

Dear @mdp0023,

sorry for the radio silence on this submission.

In the background (via email, and the JOSS editor Slack), there have been some discussions regarding the "substantial scholarly effort" criterion that we have at JOSS, and whether or not SVInsight fulfills the requirements.

These discussions were including the peer reviewers @dataspider and @bkrayfield, who brought this issue to my attention, as well as the associate editor in chief for this track, @samhforbes, who in turn also brought the discussed issues up with his colleague AEiCs.

At JOSS, we usually conduct "scope reviews" to assess whether or not a submission fulfills all requirements to proceed to peer review. In the present case, the submission was voted "in scope", however during the (deeper-diving) peer review process, several shortcomings were identified. Below, I try to summarize the most important points:

• SVInsight seems to be close to a "wrapper" around the census API with added utilities for social vulnerability scores.
• SVInsight seems to duplicate functionalities already available in other packages like the census package and factor_analyzer.
• SVInsight has issues such as unnecessary coupling of functionalities and hardcoding of data (see also Substantial scholarly effort mdp0023/SVInsight#10).

Overall, the submission was judged to require significant refactoring to become a useful utility package.

For JOSS, this presents itself as a difficult tradeoff, as on the one hand, we want peer-reviewers to point to required improvements, rather than recommending a "rejection". However, on the other hand, a major refactoring can require a lot of effort which can fall outside of the scope of a reviewer to support (reviewer burden). Some related information has been discussed here: openjournals/joss#1395

I personally agree with the assessments of the peer review process. It is unclear how we can proceed now. One option that I see is that I step down as an editor for this submission and @samhforbes finds a suitable replacement. Such a replacement would ideally be an editor with more domain knowledge for this particular submission than I have, and a willingness to go through several bigger changes as part of the review process. @samhforbes please let me know what you would prefer.

@dataspider and @bkrayfield I would be very grateful if you could communicate your intentions on whether you want to continue the peer-review here, or not. In case of the latter, we can simply unassign you from this issue.

Thank you for everyone who offered their opinion on this.
Thank you @dataspider and @bkrayfield for all the effort you have already put into the review up to this point.
And thank you for your patience @mdp0023.

[mdp0023]

We’d like to thank the editors and the reviewers for the time they have put into this review so far, and we’d like to take this opportunity to respond to some of your comments.

We believe that this package does in fact represent a significant scholarly effort as per JOSS guidelines and we would like to make that case one more time in the context of your most recent comments.

SVInsight’s functionality does not currently exist and therefore fills a need. SVInsight is intended to:

• streamline the creation of exploratory social vulnerability indices (SVIs).
• calculate SVIs from US Census data using two research supported calculation methods. One method is our own iterative factor analysis workflow that has been in development within our research group for over two years, and the second uses a rank method that was made popular by the CDC.
• allow for comparisons between SVI frameworks during the exploratory phase of research. Given user defined socio-economic variables and geographic areas of interest, unique SVIs can be calculated within seconds or minutes.

SVInsight seems to duplicate functionalities already available in other packages like the census package and factor_analyzer.

SVInsight utilizes the census and factor_analyzer to access Census data and conduct the actual factor analysis. We found that these performed well and there was no need to duplicate the work. SVInsight adds the functionality and methodology to create SVIs that these packages do not have.

SVInsight seems to be close to a "wrapper" around the census API with added utilities for social vulnerability scores.

SVInsight utilizes an existing wrapper for the Census API and adds utility for calculating social vulnerability scores, which represents the significant scholarly effort. The initial creation of these methods (i.e., to calculate an SVI for a single county) and the subsequent package took well over a year to create. With SVInsight, indices for entire states are calculated in less than a few minutes. This issue was already addressed in the pre-review of the paper.

SVInsight has issues such as unnecessary coupling of functionalities and hardcoding of data

You referenced mdp0023/SVInsight#10 and this is not hardcoding. As we responded in that thread, it is not feasible to create an SVI database of all Census areas because the SVI estimate itself is dependent on the study area and what variables are included. SVInsight gives users the flexibility to define their index (including variables and geographic extent) based on their interests. If you are referring to a different instance of hardcoding data, we would appreciate a further description of the specific issue so that we can address it.

There are two specific points on the JOSS Guidelines for what constitutes scholarly effort that we believe SVInsight falls under:

• Whether the software has already been cited in academic papers, and
• Whether the software is sufficiently useful that it is likely to be cited by other researchers working in this domain.

This package, and the methods behind it, have already been utilized in three published papers (Bixler et al., 2021, Preisser et al., 2022, Preisser et al., 2023), one under review paper, and at least two in preparation papers. The reason we sought to publish the package itself is for the intention of being able to cite the work. We additionally know that the package is being used by other research groups outside of our own. We are aware that "single-function packages are not acceptable" according to the JOSS Guidelines. While SVInsight serves a single purpose, it is not a single-function package, and it represents a streamlined package that can aid researchers in their ability to incorporate multiple iterations of custom SVIs into their own work.