[REVIEW]: medoutcon: Nonparametric efficient causal mediation analysis with machine learning in R

[whedon]

Submitting author: @nhejazi (Nima Hejazi)
Repository: https://github.com/nhejazi/medoutcon
Version: v0.1.6
Editor: @mikldk
Reviewer: @erikcs, @rrrlw
Archive: 10.5281/zenodo.5809520

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/36b2d7b95d977fa506aed40a1dd2294a/status.svg)](https://joss.theoj.org/papers/36b2d7b95d977fa506aed40a1dd2294a)

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Review checklist for @erikcs

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General checks

• Repository: Is the source code for this software available at the repository url?
• 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 (@nhejazi) 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

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 and who the target audience is?
• 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?

Review checklist for @rrrlw

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@nhejazi) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @erikcs, @rrrlw it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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@whedon commands

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

@whedon generate pdf

[whedon]

Failed to discover a Statement of need section in paper

[whedon]

Wordcount for paper.md is 1810

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.09 s (621.2 files/s, 126505.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            25           1155            319           4217
R                               11            260            790           1732
Markdown                         4            129              0            560
CSS                              3             99             48            428
TeX                              1             40              0            398
JavaScript                       3             64             32            256
Rmd                              2            109            443            144
YAML                             4             13              0             71
XML                              1              0              0             57
make                             1              9              0             20
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                            56           1878           1633           7894
-------------------------------------------------------------------------------


Statistical information for the repository 'a04a909df6ead529ae11007a' was
gathered on 2021/12/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Nima Hejazi                      5           716            364          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Nima Hejazi                 352           49.2          0.2                9.09

[whedon]

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

[whedon]

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

OK DOIs

- 10.1093/biomet/asaa085 is OK
- 10.1111/rssb.12362 is OK
- 10.5281/zenodo.1342293 is OK
- 10.1111/ectj.12097 is OK
- 10.1515/jci-2020-0018 is OK
- 10.1214/12-AOS990 is OK
- 10.2202/1557-4679.1361 is OK
- 10.21105/joss.00512 is OK
- 10.5281/zenodo.835602 is OK
- 10.1111/biom.13375 is OK
- 10.1111/add.15377 is OK

MISSING DOIs

- 10.1007/978-3-319-65304-4_14 may be a valid DOI for title: Stochastic Treatment Regimes
- 10.1111/j.1541-0420.2011.01685.x may be a valid DOI for title: Population intervention causal effects based on stochastic interventions
- 10.1515/jci-2016-0006 may be a valid DOI for title: Longitudinal mediation analysis with time-varying mediators and exposures, with application to survival outcomes
- 10.1097/ede.0000000000000034 may be a valid DOI for title: Effect decomposition in the presence of an exposure-induced mediator-outcome confounder
- 10.1515/em-2017-0007 may be a valid DOI for title: Robust and flexible estimation of stochastic mediation effects: a proposed method and example in a randomized trial setting
- 10.1007/978-1-4612-5769-1 may be a valid DOI for title: Contributions to a general asymptotic statistical theory
- 10.1007/978-1-4419-9782-1_27 may be a valid DOI for title: Cross-validated targeted minimum-loss-based estimation
- 10.1214/aos/1176350609 may be a valid DOI for title: Consistent estimation of the influence function of locally asymptotically linear estimators
- 10.1097/00001648-199203000-00013 may be a valid DOI for title: Identifiability and exchangeability for direct and indirect effects
- 10.1007/978-1-4419-9782-1_27 may be a valid DOI for title: Cross-validated targeted minimum-loss-based estimation
- 10.1257/aer.p20171038 may be a valid DOI for title: Double/debiased/neyman machine learning of treatment effects
- 10.1007/978-3-319-59626-6_5 may be a valid DOI for title: The method of path coefficients
- 10.4324/9780203994627 may be a valid DOI for title: The Logic of Scientific Discovery
- 10.1097/01.ede.0000208475.99429.2d may be a valid DOI for title: Estimation of direct causal effects

INVALID DOIs

- None

[mikldk]

Failed to discover a Statement of need section in paper

@nhejazi, I think it is fine to rename "Background and Statement of Need" to just "Statement of Need" for consistency purposes.

[mikldk]

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

OK DOIs

- 10.1093/biomet/asaa085 is OK
- 10.1111/rssb.12362 is OK
- 10.5281/zenodo.1342293 is OK
- 10.1111/ectj.12097 is OK
- 10.1515/jci-2020-0018 is OK
- 10.1214/12-AOS990 is OK
- 10.2202/1557-4679.1361 is OK
- 10.21105/joss.00512 is OK
- 10.5281/zenodo.835602 is OK
- 10.1111/biom.13375 is OK
- 10.1111/add.15377 is OK

MISSING DOIs

- 10.1007/978-3-319-65304-4_14 may be a valid DOI for title: Stochastic Treatment Regimes
- 10.1111/j.1541-0420.2011.01685.x may be a valid DOI for title: Population intervention causal effects based on stochastic interventions
- 10.1515/jci-2016-0006 may be a valid DOI for title: Longitudinal mediation analysis with time-varying mediators and exposures, with application to survival outcomes
- 10.1097/ede.0000000000000034 may be a valid DOI for title: Effect decomposition in the presence of an exposure-induced mediator-outcome confounder
- 10.1515/em-2017-0007 may be a valid DOI for title: Robust and flexible estimation of stochastic mediation effects: a proposed method and example in a randomized trial setting
- 10.1007/978-1-4612-5769-1 may be a valid DOI for title: Contributions to a general asymptotic statistical theory
- 10.1007/978-1-4419-9782-1_27 may be a valid DOI for title: Cross-validated targeted minimum-loss-based estimation
- 10.1214/aos/1176350609 may be a valid DOI for title: Consistent estimation of the influence function of locally asymptotically linear estimators
- 10.1097/00001648-199203000-00013 may be a valid DOI for title: Identifiability and exchangeability for direct and indirect effects
- 10.1007/978-1-4419-9782-1_27 may be a valid DOI for title: Cross-validated targeted minimum-loss-based estimation
- 10.1257/aer.p20171038 may be a valid DOI for title: Double/debiased/neyman machine learning of treatment effects
- 10.1007/978-3-319-59626-6_5 may be a valid DOI for title: The method of path coefficients
- 10.4324/9780203994627 may be a valid DOI for title: The Logic of Scientific Discovery
- 10.1097/01.ede.0000208475.99429.2d may be a valid DOI for title: Estimation of direct causal effects

INVALID DOIs

- None

@nhejazi Please fix these missing DOIs and let us know when you are ready for the review to start.

[mikldk]

@erikcs, @rrrlw: Thanks for agreeing to review. As you can see above, there are a few things I would like to get sorted out before you start your review. I will let you know when you can begin.

[nhejazi]

thanks for flagging these initial revisions @mikldk. these have been addressed as of the most recent commit, nhejazi/medoutcon@d0e65f5.

[mikldk]

@whedon check references

[whedon]

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

OK DOIs

- 10.1093/biomet/asaa085 is OK
- 10.1111/rssb.12362 is OK
- 10.1007/978-3-319-65304-4_14 is OK
- 10.1111/j.1541-0420.2011.01685.x is OK
- 10.1515/jci-2016-0006 is OK
- 10.1097/ede.0000000000000034 is OK
- 10.1515/em-2017-0007 is OK
- 10.5281/zenodo.1342293 is OK
- 10.1007/978-1-4612-5769-1 is OK
- 10.1007/978-1-4419-9782-1_27 is OK
- 10.1111/ectj.12097 is OK
- 10.1257/aer.p20171038 is OK
- 10.1214/aos/1176350609 is OK
- 10.1515/jci-2020-0018 is OK
- 10.1097/00001648-199203000-00013 is OK
- 10.1214/12-AOS990 is OK
- 10.2202/1557-4679.1361 is OK
- 10.21105/joss.00512 is OK
- 10.5281/zenodo.835602 is OK
- 10.1007/978-3-319-59626-6_5 is OK
- 10.4324/9780203994627 is OK
- 10.1111/biom.13375 is OK
- 10.1111/add.15377 is OK
- 10.1097/01.ede.0000208475.99429.2d is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mikldk]

@whedon generate pdf

[whedon]

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

[mikldk]

@erikcs, @rrrlw: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread.

If you have any questions or concerns please let me know.

[erikcs]

Looks good to me.

[nhejazi]

@erikcs, thanks for your review --- I've noted the issue opened and will address it at the same time as I make other changes to the package for this submission.

@rrrlw, thanks for agreeing to review this package + paper --- I'll try integrate any changes you suggest as soon as your review is available and will resolve other comments alongside yours in a single pass.

[mikldk]

@rrrlw, can you please give a brief status of your review? This is not to rush you, merely to give me an impression of the progress and time-frame.

[rrrlw]

Of course, my apologies for the delay. I’m hoping to do a first pass over the weekend.

[rrrlw]

Minor issue - after this and @erikcs's issue are resolved, looks good to go. Thank you for this contribution, @nhejazi!

[mikldk]

@whedon generate pdf

[whedon]

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

[mikldk]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2857

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2857, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

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

OK DOIs

- 10.1093/biomet/asaa085 is OK
- 10.1111/rssb.12362 is OK
- 10.1007/978-3-319-65304-4_14 is OK
- 10.1111/j.1541-0420.2011.01685.x is OK
- 10.1515/jci-2016-0006 is OK
- 10.1097/ede.0000000000000034 is OK
- 10.1515/em-2017-0007 is OK
- 10.5281/zenodo.1342293 is OK
- 10.1007/978-1-4612-5769-1 is OK
- 10.1007/978-1-4419-9782-1_27 is OK
- 10.1111/ectj.12097 is OK
- 10.1257/aer.p20171038 is OK
- 10.1214/aos/1176350609 is OK
- 10.1515/jci-2020-0018 is OK
- 10.1097/00001648-199203000-00013 is OK
- 10.1214/12-AOS990 is OK
- 10.2202/1557-4679.1361 is OK
- 10.21105/joss.00512 is OK
- 10.5281/zenodo.835602 is OK
- 10.1007/978-3-319-59626-6_5 is OK
- 10.4324/9780203994627 is OK
- 10.1111/biom.13375 is OK
- 10.1111/add.15377 is OK
- 10.1097/01.ede.0000208475.99429.2d is OK

MISSING DOIs

- None

INVALID DOIs

- None

[nhejazi]

just checking in, anything more needed from me at this point?

[mikldk]

@nhejazi Not at this point, thanks. An (associate) Editor-in-Chief will check in at some point and have a look and accept the publication if everything looks fine.

[kthyng]

Archive and version look good.

Paper comments:

• Coyle and Hejazi 2018 has a lowercase instead of uppercase "R"
• please check other capitalization in references.

[nhejazi]

thanks for going through the paper and recommending this extra pass @kthyng. I've fixed the typo you spotted as well as several others in nhejazi/medoutcon@f1a419a

[nhejazi]

@whedon generate pdf

[whedon]

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

[kthyng]

@nhejazi Ok ready to go now!

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03979 joss-papers#2865
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03979
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...

[kthyng]

Congrats on your new publication @nhejazi! Many thanks to editor @mikldk and reviewers @erikcs and @rrrlw for your time, hard work, and expertise!!

[whedon]

🎉🎉🎉 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.03979/status.svg)](https://doi.org/10.21105/joss.03979)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03979">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03979/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03979/status.svg
   :target: https://doi.org/10.21105/joss.03979

This is how it will look in your documentation:

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[nhejazi]

Thanks all for your work on reviewing and editing this paper!

[ajstewartlang]

👋 @nhejazi Might you perhaps have the bandwidth to help us out by reviewing the following submission please? I think you'll find it interesting as it seems to nicely overlap with your interests and expertise:

#5862

[nhejazi]

hi @ajstewartlang i think i can find some time to review this submission. please do note, though, that i did overlap with the author in graduate school, so i leave it to you to make sure that this is ok with JOSS policies (we have not worked together)

[ajstewartlang]

Many thanks for your openness @nhejazi - I think that overlap is fine. I'll go ahead and add you as reviewer.