[REVIEW]: GPCERF - An R package for implementing Gaussian processes for estimating causal exposure response curves

[editorialbot]

Submitting author: @Naeemkh (Naeem Khoshnevis)
Repository: https://github.com/NSAPH-Software/GPCERF
Branch with paper.md (empty if default branch): JOSS
Version: v0.2.3
Editor: @spholmes
Reviewers: @martinmodrak, @andrewherren
Archive: 10.5281/zenodo.10757333

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0128c66dd2acfec919dc435343a3d17e"><img src="https://joss.theoj.org/papers/0128c66dd2acfec919dc435343a3d17e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0128c66dd2acfec919dc435343a3d17e/status.svg)](https://joss.theoj.org/papers/0128c66dd2acfec919dc435343a3d17e)

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

@nhejazi & @martinmodrak, 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 @spholmes 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 @nhejazi

📝 Checklist for @martinmodrak

📝 Checklist for @andrewherren

[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:

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.15 s (960.8 files/s, 165910.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                       5           2099           1934           7020
HTML                            46           1525            146           5431
R                               64            604           1112           2271
Markdown                         8            285              0            993
Rmd                              6            158            300            237
YAML                             5             28             10            157
XML                              1              0              0            141
TeX                              1             15              0            114
C++                              2              9              7             52
Dockerfile                       1              6              2             22
SVG                              1              0              1             11
CSS                              2              0              0              2
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           143           4729           3512          16452
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2202

[editorialbot]

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

OK DOIs

- 10.18637/jss.v042.i08 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1007/978-1-4614-6868-4 is OK
- 10.1080/00031305.2017.1375990 is OK
- 10.1126/sciadv.aba5692 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[nhejazi]

Review checklist for @nhejazi

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/NSAPH-Software/GPCERF?
• 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 (@Naeemkh) 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?

[nhejazi]

@spholmes -- Apologies for the late realization of this, but @Naeemkh has brought to my attention that our mutual affiliation with Harvard University disqualifies me as a reviewer on account of JOSS's COI policy. In my initial reading, I'd missed the last line of the COI policy, leading to the working assumption that my service in this capacity would be acceptable since we do not and have not interacted at all outside of the context of this review.

[Naeemkh]

Hi @spholmes, I would appreciate if you could guide us regarding the next course of action for this submission. Is it possible to waive @nhejazi 's Conflict of Interest (COI) and allow him to proceed with the review process? Please inform us at your earliest convenience.

[spholmes]

Dear @Naeemkh , I will bring this up with the chief editorial team and get back to you on the COI.

[martinmodrak]

Review checklist for @martinmodrak

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/NSAPH-Software/GPCERF?
• 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 (@Naeemkh) 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?

[martinmodrak]

Review checklist for @martinmodrak

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/NSAPH-Software/GPCERF?
• 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 (@Naeemkh) 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?

[spholmes]

Hi @spholmes, I would appreciate if you could guide us regarding the next course of action for this submission. Is it possible to waive @nhejazi 's Conflict of Interest (COI) and allow him to proceed with the review process? Please inform us at your earliest convenience.

Sorry @Naeemkh , we can't waive the conflict in this case because @nhejazi and you work at the same institution. If you want to suggest some other reviewers with whom you have no connections or COI, I can ask them, I will also use the data base tomorrow to try and fill in for the next round.

[Naeemkh]

Hello @spholmes, we appreciate your update. I would also like to express our gratitude to @nhejazi for initially agreeing to undertake the review of the package.

[Naeemkh]

@spholmes, please consider Drew Herren (andrewherren) as a potential reviewer. Thanks.

[Naeemkh]

Hi @spholmes, I would be grateful if we could move faster on this submission. Thanks.

[spholmes]

Hi @Naeemkh, your message came in on the weekend and it is Tuesday morning, this is not an unusual time to respond.

[Naeemkh]

Dear @spholmes, I truly appreciate your dedication and the effort you've put into handling the submissions. I understand the intricacies of the process and the importance of thoroughness over speed. Thank you for your continued attention to the submissions.

[Naeemkh]

@spholmes, please consider Drew Herren (andrewherren) as a potential reviewer. Thanks.

[spholmes]

@andrewherren : you should be able to start the review by typing: @editorialbot generate my checklist

[Naeemkh]

@spholmes, I'd like to inquire about the review status of this submission. I understand and respect the amount of time and effort that the peer review process requires, especially considering the multiple commitments and schedules of our respected reviewers. For the purpose of planning, I was wondering if a rough timeline for the completion of the review process could be provided.
I realize it's a challenge to provide an exact timeframe due to the voluntary and often busy nature of reviewers' roles. However, any insights or a general idea of the timeline in these circumstances would be highly appreciated.
Thank you all for your attention and work in facilitating the review process of this submission. I'm looking forward to any updates.

[spholmes]

@martinmodrak

Hi Martin, @martinmodrak
Have you been able to make progress in the latter parts of the checklist during your review process.
Many thanks for the authors....

[spholmes]

@spholmes, I'd like to inquire about the review status of this submission. I understand and respect the amount of time and effort that the peer review process requires, especially considering the multiple commitments and schedules of our respected reviewers. For the purpose of planning, I was wondering if a rough timeline for the completion of the review process could be provided. I realize it's a challenge to provide an exact timeframe due to the voluntary and often busy nature of reviewers' roles. However, any insights or a general idea of the timeline in these circumstances would be highly appreciated. Thank you all for your attention and work in facilitating the review process of this submission. I'm looking forward to any updates.

@Naeemkh
I will contact the reviewers to ask them to help complete the process, for the time being, the "reviewing part" has not been accomplished.

[Naeemkh]

I will contact the reviewers to ask them to help complete the process, for the time being, the "reviewing part" has not been accomplished.

Hi @spholmes, Thank you for your swift response and for reaching out to the reviewers. I appreciate your efforts in facilitating the review process.

[editorialbot]

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

OK DOIs

- 10.18637/jss.v042.i08 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1007/978-1-4614-6868-4 is OK
- 10.1080/00031305.2017.1375990 is OK
- 10.1126/sciadv.aba5692 is OK
- 10.18637/jss.v043.i13 is OK
- 10.1515/jci-2014-0035 is OK
- 10.1515/jci-2021-0023 is OK
- 10.2202/1544-6115.1309 is OK
- 10.18637/jss.v064.i12 is OK
- 10.1111/rssb.12027 is OK
- 10.1214/17-AOAS1101 is OK
- 10.1093/biostatistics/kxu058 is OK
- 10.1080/01621459.2022.2144737 is OK
- 10.1080/01621459.2015.1044091 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: CausalGPS: An R Package for Causal Inference With ...
- No DOI given, and none found for title: Bayesian Modeling for Exposure Response Curve via ...
- No DOI given, and none found for title: wCorr: Weighted Correlations
- No DOI given, and none found for title: The Propensity Score with Continuous Treatments
- No DOI given, and none found for title: SuperLearner: Super Learner Prediction
- No DOI given, and none found for title: A Successful Git Branching Model
- No DOI given, and none found for title: logger: A Lightweight, Modern and Flexible Logging...
- No DOI given, and none found for title: GPCERF: Gaussian Processes for Estimating Causal E...
- No DOI given, and none found for title: GauPro: Gaussian Process Fitting
- No DOI given, and none found for title: mlegp: Maximum Likelihood Estimates of Gaussian Pr...
- No DOI given, and none found for title: GPfit: Gaussian Processes Modeling
- No DOI given, and none found for title: causaldrf: Estimating Causal Dose Response Functio...
- No DOI given, and none found for title: BCEE: The Bayesian Causal Effect Estimation Algori...
- No DOI given, and none found for title: bkmr: Bayesian Kernel Machine Regression
- No DOI given, and none found for title: CBPS: Covariate Balancing Propensity Score
- No DOI given, and none found for title: npcausal [R package]

INVALID DOIs

- None

[editorialbot]

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

C) \textasciitilde log10(n))
                   ^
unexpected control sequence \textasciitilde
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

C) \textasciitilde log10(n))
                   ^
unexpected control sequence \textasciitilde
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

[editorialbot]

👋 @openjournals/bcm-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#5119, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@Naeemkh As AEiC I will now help process the final steps towards acceptance in JOSS. I have checked the archive link, this review, the paper, and your repository. Most seems in order. I only have the below points that require your attention:

• Please add this DOI for the arXiv article: 10.48550/arXiv.2105.03454
• I see you have (and link to) a code of conduct. However I do not see specific contribution guidelines. Perhaps consider adding a CONTRIBUTING.md file and linking to it from the README. This website has some examples: https://contributing.md/example/

[Kevin-Mattheus-Moerman]

@andrewherren thanks for your review here. I see you have some boxes unticked. Could you tick these if they can be ticked, or otherwise clarify why they are not? Thanks!

[Kevin-Mattheus-Moerman]

@editorialbot remove @nhejaz as reviewer

[editorialbot]

@nhejaz is not in the reviewers list

[Kevin-Mattheus-Moerman]

@editorialbot remove @nhejazi as reviewer

[editorialbot]

@nhejazi removed from the reviewers list!

[Naeemkh]

Hi @Kevin-Mattheus-Moerman, thanks for the comments. I added DOI for the mentioned paper, and also added contributing document. Best regards, Naeem.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[andrewherren]

@Kevin-Mattheus-Moerman Sorry about that, just ticked off the remaining boxes! Thanks for following up.

[Kevin-Mattheus-Moerman]

@Naeemkh apologies, just spotted another arXiv DOI to add: 10.48550/arXiv.2310.00561

[Naeemkh]

Hi @Kevin-Mattheus-Moerman, thanks for letting me know. I just fixed it.

[Kevin-Mattheus-Moerman]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

C) \textasciitilde log10(n))
                   ^
unexpected control sequence \textasciitilde
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

C) \textasciitilde log10(n))
                   ^
unexpected control sequence \textasciitilde
expecting "%", "\\label", "\\tag", "\\nonumber" or whitespace

[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: Khoshnevis
  given-names: Naeem
  orcid: "https://orcid.org/0000-0003-4315-1426"
- family-names: Ren
  given-names: Boyu
  orcid: "https://orcid.org/0000-0002-5300-1184"
- family-names: Braun
  given-names: Danielle
  orcid: "https://orcid.org/0000-0002-5177-8598"
contact:
- family-names: Khoshnevis
  given-names: Naeem
  orcid: "https://orcid.org/0000-0003-4315-1426"
doi: 10.5281/zenodo.10757333
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Khoshnevis
    given-names: Naeem
    orcid: "https://orcid.org/0000-0003-4315-1426"
  - family-names: Ren
    given-names: Boyu
    orcid: "https://orcid.org/0000-0002-5300-1184"
  - family-names: Braun
    given-names: Danielle
    orcid: "https://orcid.org/0000-0002-5177-8598"
  date-published: 2024-03-13
  doi: 10.21105/joss.05465
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5465
  title: GPCERF - An R package for implementing Gaussian processes for
    estimating causal exposure response curves
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05465"
  volume: 9
title: GPCERF - An R package for implementing Gaussian processes for
  estimating causal exposure response curves

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.05465 joss-papers#5126
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05465
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...

[Kevin-Mattheus-Moerman]

@Naeemkh congratulations on this JOSS publication!

I would like to thank @spholmes for editing!

And a special thanks to the reviewers: @martinmodrak, @andrewherren !!!

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05465/status.svg)](https://doi.org/10.21105/joss.05465)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05465">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05465/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05465/status.svg
   :target: https://doi.org/10.21105/joss.05465

This is how it will look in your documentation:

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