[REVIEW]: findSVI: an R package to calculate the Social Vulnerability Index at multiple geographical levels

[editorialbot]

Submitting author: @heli-xu (Heli Xu)
Repository: https://github.com/heli-xu/findSVI
Branch with paper.md (empty if default branch): joss-paper
Version: v0.1.2
Editor: @osorensen
Reviewers: @epiben, @mashrur-ayon
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f488cf0b6f9f71740f6fde956059355b/status.svg)](https://joss.theoj.org/papers/f488cf0b6f9f71740f6fde956059355b)

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

@epiben & @mashrur-ayon, 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 @osorensen 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 @epiben

📝 Checklist for @mashrur-ayon

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1601.5 files/s, 205912.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               16            508            522           1562
Rmd                              6            179            291            474
TeX                              1             37              0            275
CSV                              4              0              0            272
Markdown                         4             48              0            208
YAML                             4             19              9             96
-------------------------------------------------------------------------------
SUM:                            35            791            822           2887
-------------------------------------------------------------------------------

Commit count by author:

   158	Heli Xu
     2	heli-xu

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 834

✅ 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 📄 👈

[editorialbot]

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

OK DOIs

- 10.1016/j.jamcollsurg.2020.11.024 is OK
- 10.1016/j.surg.2021.06.001 is OK
- 10.1016/j.ijdrr.2020.101517 is OK
- 10.1016/j.cpcardiol.2022.101182 is OK
- 10.1016/j.amepre.2020.06.006 is OK
- 10.1007/s11606-020-05882-3 is OK
- 10.1111/puar.13264 is OK
- 10.7326/M20-3936 is OK
- 10.1136/bmjopen-2020-048086 is OK
- 10.1016/j.lana.2022.100220 is OK
- 10.1093/aje/kwac076 is OK
- 10.1016/j.socscimed.2022.115307 is OK

MISSING DOIs

- No DOI given, and none found for title: CDC/ATSDR SVI data and documentation download
- No DOI given, and none found for title: tidycensus: Load US Census Boundary and Attribute ...
- No DOI given, and none found for title: Measuring community vulnerability to natural and a...
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation
- No DOI given, and none found for title: purrr: Functional Programming Tools
- No DOI given, and none found for title: stringr: Simple, Consistent Wrappers for Common St...
- No DOI given, and none found for title: tidyr: Tidy Messy Data
- No DOI given, and none found for title: tidyselect: Select from a Set of Strings
- No DOI given, and none found for title: rlang: Functions for Base Types and Core R and ’Ti...
- No DOI given, and none found for title: cli: Helpers for Developing Command Line Interface...

INVALID DOIs

- https://doi.org/10.2202/1547-7355.1792 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41591-021-01379-6 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1038/s41467-023-38084-6 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.jacadv.2023.100577 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1161/CIRCULATIONAHA.121.054516 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.hjdsi.2021.100611 is INVALID because of 'https://doi.org/' prefix
- http://dx.doi.org/10.15585/mmwr.mm7012e1 is INVALID because of 'https://doi.org/' prefix

[epiben]

Review checklist for @epiben

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/heli-xu/findSVI?
• 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 (@heli-xu) 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?

[osorensen]

👋 @mashrur-ayon can you please update us on how it's going with your review?

[osorensen]

👋 @epiben, @mashrur-ayon, can you please update us on how it's going with your reviews?

[mashrur-ayon]

@editorialbot commands

[editorialbot]

Hello @mashrur-ayon, 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

[mashrur-ayon]

Review checklist for @mashrur-ayon

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/heli-xu/findSVI?
• 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 (@heli-xu) 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?

[osorensen]

@mashrur-ayon, I notice you generated your review checklist. Please let me know if you have any questions about how to conduct the review.