[REVIEW]: inAccessMod: An R package to automate data downloading and processing for AccessMod

[editorialbot]

Submitting author: @ptimoner (Pablo Timoner)
Repository: https://github.com/unige-geohealth/inAccessMod
Branch with paper.md (empty if default branch):
Version: v1.1
Editor: @arfon
Reviewers: @ConnorDonegan, @mponce0
Archive: 10.5281/zenodo.10466894

Status

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Markdown: [![status](https://joss.theoj.org/papers/dcacbc017b2751c190e5472d1d7e2b02/status.svg)](https://joss.theoj.org/papers/dcacbc017b2751c190e5472d1d7e2b02)

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

@ConnorDonegan & @mponce0, 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 @arfon 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 @ConnorDonegan

📝 Checklist for @mponce0

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (2316.7 files/s, 201929.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               50             57            914           3212
TeX                              1             27              0            160
Markdown                         2             17              0             90
Rmd                              1            105            157             32
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            55            207           1075           3512
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 802

[editorialbot]

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

OK DOIs

- 10.1186/1476-072X-7-63 is OK
- 10.1016/j.lansea.2022.100103 is OK
- 10.1371/journal.pgph.0000626 is OK
- 10.1136/bmjopen-2020-039138 is OK
- 10.1186/s12889-020-09486-8 is OK
- 10.1016/S2214-109X(17)30488-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[arfon]

@ConnorDonegan, @mponce0 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. Please create your checklist typing:

@editorialbot generate my checklist

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/5879 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.

[editorialbot]

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

[ConnorDonegan]

Review checklist for @ConnorDonegan

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/unige-geohealth/inAccessMod?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ptimoner) 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?

[arfon]

👋 @mponce0 – just checking when you might be able to start on your review?

[mponce0]

👋 @mponce0 – just checking when you might be able to start on your review?

Thank your patience and the reminder, will be done shortly

[mponce0]

Review checklist for @mponce0

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/unige-geohealth/inAccessMod?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@ptimoner) 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?

[mponce0]

@arfon I'm done with the review.

I'm including some additional elements for the authors that could help address some of the missing points:

General checks

• Contribution and authorship: Has the submitting author (@ptimoner) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

@ptimoner appears to be the main contributor to the repository.
However, it is not clear the role of each of the authors in the paper/package, a statement of contribution can help with this.

Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

The package appears to build upon a well established open source tool in the field modelling health care access.
It looks to be a sort of wrapper to provide quick access to the data and models from this former tool.

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.

As the paper is based on health care access data, although the package itself does not contain it but gives access to it... I'm not sure whether we should look deeper into this?

Functionality

Installation: Does installation proceed as outlined in the documentation?

Not specified in the paper, but is an R package so it should follow the usual standards, still borth menitoning it.

Functionality: Have the functional claims of the software been confirmed?

Can not verify that, as no examples are provided.

Documentation

Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.

Partially, nothing is mentioned in the manuscript but instructions can be found in the package github repository.

Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).

No examples are included, I would strongly suggest to do so.

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

Partially, a very high level overview is described in the manuscript.

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

No

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

No specifications neither about contributions nor support are provided.

Software paper

State of the field: Do the authors describe how this software compares to other commonly-used packages?

No comparison is done with other packages nor mentioned whether there is a similar package other than the "mother" tool used to harvest the data from.

---

Further recommendations:

• submit to CRAN

• add examples

---

[ptimoner]

@mponce0 Thanks a lot for taking time to review our package. Regarding the documentation and functionality sections, I just wanted to mention that there is vignette available. Following @ConnorDonegan recommendations (unige-geohealth/inAccessMod#4), we added the instructions to the README file so users know how to obtain the vignette, we modified the vignette, and it is now possible to move from "initiate_project" (first step) to "compile_processed_data" (last step) just following the Tutorial, using the same example project across the different functions. We also added example codes to the help pages, and we added example data within the package for the additional functions (multi_ts and hf_best_cov), the ones that can be run outside the main pipeline, and that can be useful for AccessMod users. This way, the user can test the functions even they don't have their own inputs. I hope that this clarifies the main concern raised in your review.
Thanks again,
Best,
Pablo

[mponce0]

Hi Pablo @ptimoner , thanks for the clarification, this helps.
However, I wonder are you planning on submitting the packages to CRAN or bioconductor?
If the answer is not maybe it would be worth it presenting the tutorial and examples as a main addition to the repo, vignettes make a lot of sense for R package but really useful when hosted on the main R repositories as are web-rendered and provide easy access for the users... in your case you could do the same by just offering a markdown or PDF version in your repository again unless your plans are to submit to CRAN/bioconductor.

WRT installation instructions, I have been having some issues installing the package.
For instance,

-----------------------------------
ERROR: this R is version 4.1.2, package 'inAccessMod' requires R >=  4.1.3
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'inAccessMod' from GitHub:
! System command 'R' failed
In addition: There were 13 warnings (use warnings() to see them)

as indicated in the instructions section, this type of things and other dependencies should be mentioned.

Similarly, when trying to install the package in R v 4.3.2, some missing dependencies are making the installation fail, e.g.

ERROR: dependencies ‘crsuggest’, ‘exactextractr’, ‘gdalUtils’, ‘osmextract’, ‘rgdal’, ‘rgeoboundaries’, ‘rgeos’, ‘sf’ are not available for package ‘inAccessMod’

[ptimoner]

Dear Marcelo @mponce0,

Thanks for pointing out the importance of having all installation details in the README and a quickly accessible vignette in the main repository. I followed your suggestion and made the required changes. I invite you to revise the modified README and to check the new TUTORIAL file in the main repository.

Thanks again,

Best regards,

Pablo

[ConnorDonegan]

@ptimoner Can you comment on the issue of automated tests?

If you don't have something already in use, can you create an automated test to guard against future issues being introduced with changes to the code or dependencies? (Not necessarily using https://testthat.r-lib.org/) The tutorial now verifies that the code runs, but I would be more confident if I could see some code that will help prevent future issues.

As a review criteria we have to consider this:

• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

[ptimoner]

@ConnorDonegan Thank you for your valuable insights. While our tutorial already outlines the manual steps required to verify the package's functionality, to strengthen our validation process, I've integrated automated tests for both individual functions and the complete pipeline into the package. In addition to this, I've included instructions in the README on how to execute these tests.
I hope that these enhancements will address your concerns more effectively and provide comprehensive assurance about the package's functionality.

Thanks again,

Best regards,

Pablo

[arfon]

@ptimoner – it looks like there are some suggested improvements to your paper too. Have you made those?

[ptimoner]

@arfon Indeed, we added an author contribution statement and a short installation guidelines as suggested by @mponce0 in the paper. Thanks.

[arfon]

@ConnorDonegan, @mponce0 – the author (@ptimoner) has made a number of updates to the software and paper since your initial reviews. Could I ask that you both revisit this package and update your checklists accordingly?

Many thanks, Arfon

[ConnorDonegan]

Hi @ptimoner I'm having trouble getting the tests to run. I think its not able to find the files. My memory of it is that the tests have to be placed in a tests/testthat/ folder.

I see that the review criteria asks for autormated or manual tests, and the new vignette meets the latter criteria. I think it would be valuable to see the new automated tests run cleanly to help catch new issues as the code base changes, although its not necessary for meeting review criteria. Thanks for your responsiveness.

The paper

As is, it follows the JOSS style---very concise, documents the need for the software and its main functionality. I think it could benefit from

• referencing some of the alternative methods/software for completing the same tasks (i.e., some specific GIS software)
• possibly a figure or illustration of some kind (e.g., of the required folder/file structure it produces)
• the references for WHO reports may need URLs or additional information
• Note on contributor guidelines and where to go for help/issues/pull requests

[ptimoner]

Hi @ConnorDonegan,

Thanks for your comments. I changed the path of my test files, and now it should work with devtools::test().

Regarding the further comments on the paper:

1. To our knowledge, there is no alternative software for completing the same tasks the way we do here; the downloading is usually done manually, and the GIS operations are usually also performed manually using any GIS software. For this reason we decided to keep it broad and just mention that "the different GIS operations involved in pre-processing these input layers can be time-consuming and might cause issues with data consistency and quality".

2. As suggested, we added in the paper a figure that illustrates the folder/file structure the functions produce.

3. We added a reference for HeRAMS/WHO in the paper.

4. We added contributor guidelines in the README.

Thanks for taking the time to review our paper/package and for your valuable feedback.

Best regards,

Pablo

[ConnorDonegan]

Thanks, this looks good. The last thing I'm doing for my review (presently) is starting up AccessMod to verify that I can successfully bring the data into the application.

[editorialbot]

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

[ptimoner]

Thanks @mponce0 for pointing out this issue of the failed automated tests. It has been addressed (unige-geohealth/inAccessMod#5 (comment)) and they should work now. As suggested, I also mentioned in the README and the Tutorial that the user must have a working internet connection in order to access all the functions that allow downloading data.

Best regards,

Pablo

[arfon]

Thanks for the additional iterations here folks, including moving to a more 'robust' set of dependencies. @mponce0 – I think we're waiting on you at this point to verify that you can now run the tests.

[mponce0]

Alright, all good from my side now!
I'd still encourage the authors to consider submitting the package to CRAN, it will definitely help streamlining the process of CD/CI and gain visibility among the R community.

[ptimoner]

Dear @arfon,
I am writing to inquire about the current status of our paper. I would like to kindly request an update on the review process and whether there is any further information or actions required from our side.
Thanks a lot,
Best regards,
Pablo

[arfon]

@ptimoner – looks like we're very close to being done here. I will circle back here next week, but in the meantime, please give your own paper a final read to check for any potential typos etc.

After that, could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
• I can then move forward with accepting the submission.

[ptimoner]

@arfon We gave our paper a final read, we did not find any typo and no change has been made.
We made a new release (v1.1), and upload the archive in Zenodo making sure that the title and the authors correspond to our paper.
Here is the DOI: 10.5281/zenodo.10466894
Here the link to the record in zenodo: https://zenodo.org/records/10466894
Thanks a lot,
Best regards,
Pablo

[arfon]

@editorialbot set v1.1 as version

[editorialbot]

Done! version is now v1.1

[arfon]

@editorialbot set 10.5281/zenodo.10466894 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10466894

[arfon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1186/1476-072X-7-63 is OK
- 10.1016/j.lansea.2022.100103 is OK
- 10.1371/journal.pgph.0000626 is OK
- 10.1136/bmjopen-2020-039138 is OK
- 10.1186/s12889-020-09486-8 is OK
- 10.1016/S2214-109X(17)30488-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#4882, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Timoner
  given-names: Pablo
  orcid: "https://orcid.org/0000-0003-4757-4928"
- family-names: Hierink
  given-names: Fleur
  orcid: "https://orcid.org/0000-0002-2727-0540"
- family-names: Baecher
  given-names: Loïc
- family-names: Fuhrer
  given-names: Caroline
- family-names: Ray
  given-names: Nicolas
  orcid: "https://orcid.org/0000-0002-4696-5313"
contact:
- family-names: Timoner
  given-names: Pablo
  orcid: "https://orcid.org/0000-0003-4757-4928"
doi: 10.5281/zenodo.10466894
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Timoner
    given-names: Pablo
    orcid: "https://orcid.org/0000-0003-4757-4928"
  - family-names: Hierink
    given-names: Fleur
    orcid: "https://orcid.org/0000-0002-2727-0540"
  - family-names: Baecher
    given-names: Loïc
  - family-names: Fuhrer
    given-names: Caroline
  - family-names: Ray
    given-names: Nicolas
    orcid: "https://orcid.org/0000-0002-4696-5313"
  date-published: 2024-01-07
  doi: 10.21105/joss.05879
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5879
  title: "inAccessMod: An R package to automate data downloading and
    processing for AccessMod"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05879"
  volume: 9
title: "inAccessMod: An R package to automate data downloading and
  processing for AccessMod"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05879 joss-papers#4886
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05879
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@ConnorDonegan, @mponce0 – many thanks for your reviews here! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@ptimoner – your paper is now accepted and published in JOSS ⚡🚀💥

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[ptimoner]

@arfon Thanks a lot for taking care of the review process. @mponce0 @ConnorDonegan thanks to you for all your valuable insights.
Best,
Pablo