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

whedon commented 2 years ago

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

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Review checklist for @erikcs

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Conflict of interest

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General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 2 years ago

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 :tada:.

:warning: JOSS reduced service mode :warning:

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whedon commented 2 years ago

Failed to discover a Statement of need section in paper

whedon commented 2 years ago

Wordcount for paper.md is 1810

whedon commented 2 years ago

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 commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

@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 commented 2 years ago

thanks for flagging these initial revisions @mikldk. these have been addressed as of the most recent commit, https://github.com/nhejazi/medoutcon/commit/d0e65f5df58b5f5bf9917ad0a4766e343d50599d.

mikldk commented 2 years ago

@whedon check references

whedon commented 2 years ago

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 commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikldk commented 2 years ago

@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 commented 2 years ago

Looks good to me.

nhejazi commented 2 years ago

@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 commented 2 years ago

@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 commented 2 years ago

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

rrrlw commented 2 years ago

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

whedon commented 2 years ago

:wave: @rrrlw, please update us on how your review is going (this is an automated reminder).

nhejazi commented 2 years ago

The points of improvement brought up in issues 31, 32, and 33 have been addressed in PR 34. Thanks very much @erikcs and @rrrlw for your timely and diligent reviews!

@mikldk I’ve left PR 34 open in case you might have any final revision comments. If not (or if everything looks in order), I’ll go ahead and merge that PR.

mikldk commented 2 years ago

@nhejazi I think you can just go ahead and merge. I see that you have updated the package title. Is the title of the paper also updated (if necessary)?

nhejazi commented 2 years ago

Great! Thanks for the quick confirmation @mikldk. I just merged the PR and can take other steps (e.g., minting a release DOI) as needed. I've only shortened the package title and would like to keep the paper title a bit more general, so I think that can stay as is. I did also introduce a minor version bump 0.1.5 -> 0.1.6, and I think the version of the package referenced in the opening comment of this issue should reflect that.

mikldk commented 2 years ago

@whedon set v0.1.6 as version

whedon commented 2 years ago

OK. v0.1.6 is the version.

mikldk commented 2 years ago

@rrrlw Can you confirm that the license issue has been resolved (and check the corresponding box at the top of this issue)?

rrrlw commented 2 years ago

Looks good, done. Thanks for your contribution, @nhejazi!

mikldk commented 2 years ago

@nhejazi :

Please have a final read though of the paper, checking language etc.
Have a final check of the proofs with @whedon generate pdf
In general, be sure that all versions are correct and that the repo is in the state that should be published.
Please make a tagged release and archive (e.g. with Zenodo) as described here, and report the version number and archive DOI in this thread. Please verify that the archive deposit has the correct metadata (title and author list), or edit these if that is not the case.

nhejazi commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

nhejazi commented 2 years ago

Thanks, @mikldk -- I've completed a final pass through the paper and package documentation, making minor fixes throughout. The PDF created by whedon looks good to me, so I went ahead and created a GitHub release (https://github.com/nhejazi/medoutcon/releases/tag/joss) and archived that release via Zenodo (https://zenodo.org/record/5809520). The archived package has version number 0.1.6 with DOI 10.5281/zenodo.5809520. Please let me know if there's anything else I need to do/fix.

nhejazi commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

nhejazi commented 2 years ago

alright, all LGTM after that last pass through the materials

mikldk commented 2 years ago

@whedon set 10.5281/zenodo.5809520 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5809520 is the archive.

mikldk commented 2 years ago

@whedon check references

mikldk commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikldk commented 2 years ago

@nhejazi Can you add countries to the affiliations in the paper?

nhejazi commented 2 years ago

Sure @mikldk, just added them here

nhejazi commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikldk commented 2 years ago

@whedon check references

whedon commented 2 years ago

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 commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mikldk commented 2 years ago

@whedon recommend-accept

openjournals / joss-reviews