[REVIEW]: snSMART: An R Package for Small Sample, Sequential, Multiple Assignment, Randomized Trial Data Analysis

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@sidiwang@osorensen<!--end-editor-- Reviewers: @aghaynes, @ezraporter Archive: 10.5281/zenodo.13370298

Status

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Markdown: [![status](https://joss.theoj.org/papers/119f9b14b157f475c25f737aca4a166e/status.svg)](https://joss.theoj.org/papers/119f9b14b157f475c25f737aca4a166e)

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

@aghaynes & @ezraporter, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @aghaynes

📝 Checklist for @ezraporter

editorialbot commented 4 months ago

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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 commented 4 months ago

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

OK DOIs

- 10.1016/j.cct.2020.105989 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

MISSING DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

INVALID DOIs

- 10.1111/rssc.1246 is INVALID

editorialbot commented 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (993.3 files/s, 250890.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               10            436            929           2128
Markdown                         3            132              0            699
TeX                              1             33              1            195
YAML                             4             17              9            102
Rmd                              1             18             63             37
-------------------------------------------------------------------------------
SUM:                            19            636           1002           3161
-------------------------------------------------------------------------------

Commit count by author:

   117  Sidi Wang
    31  sidiwang
    13  Michael Kleinsasser
     1  Michael (Mike) Kleinsasser

editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 1205

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago

License info:

🟡 License found: GNU General Public License v2.0 (Check here for OSI approval)

editorialbot commented 4 months ago

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

aghaynes commented 4 months ago

Review checklist for @aghaynes

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 https://github.com/sidiwang/snSMART?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@sidiwang) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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, who the target audience is, and its relation to other work?
[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?

aghaynes commented 4 months ago

I have made some comments in the issue here which address the unchecked points above as well as some other points and (non-mandatory) recommendations

osorensen commented 4 months ago

Thanks for your review @aghaynes. @sidiwang, you are welcome to start addressing these issues right away. Please report here when done, or if you have any questions.

aghaynes commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

aghaynes commented 3 months ago

@sidiwang has addressed the vaste majority of my comments and has just one or two minor things to do.

osorensen commented 3 months ago

👋 @ezraporter could you please update us on how it's going with your review?

ezraporter commented 3 months ago

Sorry for the delay! I'm working on it now and expect to be done tomorrow

ezraporter commented 3 months ago

Review checklist for @ezraporter

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 https://github.com/sidiwang/snSMART?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@sidiwang) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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, who the target audience is, and its relation to other work?
[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?

ezraporter commented 3 months ago

My comments have been addressed by @sidiwang. All good on my end

osorensen commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

osorensen commented 3 months ago

@sidiwang I've open to pull requests with small suggested changes to the paper. Please ping me here when they're fixed.

sidiwang commented 3 months ago

Hi @osorensen,

Thank you for your suggestions! I have made the changes. Please take a look and let me know if further adjustments are needed.

Thanks, Sidi

osorensen commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

osorensen commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

✅ OK DOIs

- 10.1016/j.cct.2020.105989 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.1111/rssc.1246 is INVALID

osorensen commented 3 months ago

@sidiwang, thanks. It seems like the reference to Chao et al. (2020) has an error in the DOI. The correct DOI is 10.1111/rssc.12406. Could you please update?

sidiwang commented 3 months ago

@osorensen Just fixed that! Thank you :)

osorensen commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

✅ OK DOIs

- 10.1016/j.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

osorensen commented 3 months ago

@sidiwang

At this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

sidiwang commented 3 months ago

Hi @osorensen,

I just made a tagged release, the version is 0.2.4, and the DOI is 10.5281/zenodo.13370298

I hope everything was done correctly. Please let me know if there’s anything that needs adjustment.

Thanks, Sidi

osorensen commented 3 months ago

@editorialbot set 0.2.4 as version

editorialbot commented 3 months ago

Done! version is now 0.2.4

osorensen commented 3 months ago

@editorialbot set 10.5281/zenodo.13370298 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.13370298

osorensen commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

✅ OK DOIs

- 10.1016/j.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 3 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element tbody content does not follow the DTD, expecting (tr)+, got ()

osorensen commented 3 months ago

@openjournals/dev can you help us with the issue above?

arfon commented 3 months ago

Looks like there's some issue with the generated JATS file: https://github.com/openjournals/joss-papers/blob/bcb1737a9ecc52b458bd1019dd24fa82f36d10e6/joss.06971/paper.jats/10.21105.joss.06971.jats

I think it's the table in the document. @sidiwang – could you please try updating your table to be strictly Markdown formatted one?

sidiwang commented 3 months ago

@arfon @osorensen Thank you for the feedback. I just made some changes. Could you take a look and see whether it works now? Thanks a lot.

osorensen commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

✅ OK DOIs

- 10.1016/j.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/sbcs-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5843, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

samhforbes commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago

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

✅ OK DOIs

- 10.1016/j.cct.2020.105989 is OK
- 10.1111/rssc.12406 is OK
- 10.1002/sim.7900 is OK
- 10.1080/10543406.2020.1815032 is OK
- 10.1002/sim.8813 is OK
- 10.1002/sim.8776 is OK
- 10.1016/S0140-6736(02)07283-5 is OK
- 10.1186/s13063-020-04285-3 is OK
- 10.2307/2348770 is OK
- 10.1111/1467-985X.00154 is OK
- 10.1002/sim.2022 is OK
- 10.1093/biostatistics/kxr016 is OK
- 10.32614/CRAN.package.geepack is OK
- 10.18637/jss.v015.i02 is OK
- 10.1002/sim.1650 is OK
- 10.2307/2531248 is OK
- 10.32614/CRAN.package.EnvStats is OK
- 10.32614/CRAN.package.rjags is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: geepack: Yet Another Package for Generalized Estim...
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

samhforbes commented 2 months ago

Hi @sidiwang I noticed your software licence doesn't match the licence in your archive. Can you update to make sure both use a OSI approved licence and that it matches please?

sidiwang commented 2 months ago

Hi @samhforbes I just updated the license in my archive. Hopefully, I did it the right way! Thank you!

samhforbes commented 2 months ago

@editorialbot recommend-accept

openjournals / joss-reviews