[PRE REVIEW]: rbmi: A R package for standard and reference-based multiple imputation methods

[editorialbot]

Submitting author: !--author-handle-->@nociale<!--end-author-handle-- (Alessandro Noci) Repository: https://github.com/insightsengineering/rbmi Branch with paper.md (empty if default branch): Version: 1.1.0 Editor: !--editor-->@fboehm<!--end-editor-- Reviewers: @DanielRivasMD, @JoranTiU Managing EiC: Kevin M. Moerman

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (923.8 files/s, 262988.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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R                               65           3675           3808          12471
HTML                             3            104              6           2847
TeX                              2            101              0            768
Markdown                         5            188              0            649
Rmd                              3            395            761            452
YAML                            12            105             15            446
SAS                              1             36             22             81
Dockerfile                       1              8              0             47
Bourne Shell                     1              4              1             34
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C/C++ Header                     1              0              1              0
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SUM:                            95           4616           4614          17816
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 940

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- 10.1093/biomet/86.4.948 may be a valid DOI for title: Miscellanea. Small-sample degrees of freedom with multiple imputation
- 10.1177/0962280220932189 may be a valid DOI for title: Bootstrap inference for multiple imputation under uncongeniality and misspecification
- 10.1002/(sici)1097-0258(20000515)19:9<1141::aid-sim479>3.0.co;2-f may be a valid DOI for title: Bootstrap confidence intervals: when, which, what? A practical guide for medical statisticians
- 10.1080/10543406.2013.834911 may be a valid DOI for title: Analysis of longitudinal trials with protocol deviation: a framework for relevant, accessible assumptions, and inference via multiple imputation
- 10.1111/rssa.12423 may be a valid DOI for title: Information-anchored sensitivity analysis: Theory and application
- 10.1002/sim.8569 may be a valid DOI for title: Sensitivity analysis for clinical trials with missing continuous outcome data using controlled multiple imputation: a practical guide
- 10.1002/pst.2019 may be a valid DOI for title: The attributable estimand: a new approach to account for intercurrent events
- 10.1080/07474930008800459 may be a valid DOI for title: Bootstrap tests: How many bootstraps?
- 10.1080/19466315.2020.1736141 may be a valid DOI for title: The Use of a Variable Representing Compliance Improves Accuracy of Estimation of the Effect of Treatment Allocation Regardless of Discontinuation in Trials with Incomplete Follow-up
- 10.1111/j.1540-5907.2010.00447.x may be a valid DOI for title: What to do about missing values in time-series cross-section data
- 10.1214/aos/1043351257 may be a valid DOI for title: A unified jackknife theory for empirical best prediction with M-estimation
- 10.1080/10543406.2015.1094810 may be a valid DOI for title: On analysis of longitudinal clinical trials with missing data using reference-based imputation
- 10.1177/009286150804200402 may be a valid DOI for title: Recommendations for the primary analysis of continuous endpoints in longitudinal clinical trials
- 10.1177/2168479019836979 may be a valid DOI for title: Aligning estimators with estimands in clinical trials: putting the ICH E9 (R1) guidelines into practice
- 10.1214/ss/1177010269 may be a valid DOI for title: Multiple-imputation inferences with uncongenial sources of input
- 10.1093/biomet/58.3.545 may be a valid DOI for title: Recovery of inter-block information when block sizes are unequal
- 10.1080/19466315.2019.1689845 may be a valid DOI for title: Aligning Treatment Policy Estimands and Estimators—A Simulation Study in Alzheimer’s Disease
- 10.1080/10543406.2014.928306 may be a valid DOI for title: Comment on “Analysis of longitudinal trials with protocol deviations: A framework for relevant, accessible assumptions, and inference via multiple imputation,” by Carpenter, Roger, and Kenward
- 10.1080/10543401003777995 may be a valid DOI for title: MMRM versus MI in dealing with missing data—a comparison based on 25 NDA data sets
- 10.1177/0962280216683570 may be a valid DOI for title: Should multiple imputation be the method of choice for handling missing data in randomized trials?
- 10.1111/biom.12702 may be a valid DOI for title: On the multiple imputation variance estimator for control-based and delta-adjusted pattern mixture models
- 10.1214/20-sts793 may be a valid DOI for title: Maximum likelihood multiple imputation: Faster imputations and consistent standard errors without posterior draws
- 10.1093/biomet/85.4.935 may be a valid DOI for title: Large-sample theory for parametric multiple imputation procedures
- 10.1080/10543406.2019.1684308 may be a valid DOI for title: A causal modelling framework for reference-based imputation and tipping point analysis in clinical trials with quantitative outcome

INVALID DOIs

- None

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@nociale thanks for this submission. I am the AEiC on call for the coming week and will be looking for a handling editor. In the meantime perhaps you can address those potentially missing DOIs :point_up: , you can update the paper by calling @editorialbot generate pdf and you can use @editorialbot check references to check those DOIs again.

[Kevin-Mattheus-Moerman]

@nociale I have just assigned the waitlisted label here. This is because it appears all editors in this domain are currently handling many other submission. We will assign an editor once one becomes available.

[kthyng]

Hi @fboehm, are you interested in editing this submission?

[kthyng]

@editorialbot invite @fboehm as editor

[editorialbot]

Invitation to edit this submission sent!

[fboehm]

Yes, @kthyng , I'm happy to edit this submission.

Thank you!

[fboehm]

@editorialbot assign @fboehm as editor

[editorialbot]

Assigned! @fboehm is now the editor

[fboehm]

@editorialbot list reviewers

[editorialbot]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[fboehm]

@JoranTiU, @stmcg, @DanielRivasMD, @jaybee84 - would any of you be willing to review this submission to JOSS? The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.html

Editors and reviewers post comments on the Review issue, and authors respond to the comments and improve their submission until acceptance (or withdrawal, if they feel unable to satisfy the review).

[DanielRivasMD]

@fboehm I can take a look. First time on this journal so some guidance and / or advice would be appreciated along the way

[fboehm]

Thanks, @DanielRivasMD ! If you decide that you'd like to review this, please let me know. I'm happy to guide you through the process of reviewing for JOSS. You would need to install the R package and verify its functionality. You would also need to read the accompanying paper and ensure that it meets specified expectations. If you decide to review this submission, I'll prepare a standard checklist for you to complete. Unlike many journals, you are not expected to write a document that contains your review for the JOSS submission. Instead, you merely complete a checklist. A JOSS review is an iterative process, so you'll first download and install the R package and try to run it. Perhaps something won't work as indicated, in which case you'd tell the authors about it via our review thread. Nearly every submission that gets reviewed eventually gets published, once the reviewers are satisfied with any needed modifications. I hope that this helps.

[fboehm]

To get a sense of the checklist items, please see this ongoing review: https://github.com/openjournals/joss-reviews/issues/4242

[fboehm]

Please note, @DanielRivasMD , that you don't need to do anything until I ask you to do it. If you decide to review, it would be a few days before we start the review process, since I'll need to find a second reviewer. We typically ask that you complete the first round of review within about a month.

[DanielRivasMD]

Sounds great! Let's do it! I read the article, and will install and test the software, is this the review thread where I should comment? Or where can I find it?

[DanielRivasMD]

Ahhh great! Good to know. I'll wait for further instructions then

[fboehm]

Thanks, @DanielRivasMD ! The review thread doesn't exist yet - I'll make it once we find a second reviewer. In the mean time, if you have comments to share with me or the authors, please feel free to share them here. We'll then switch over to the review thread once I find a second reviewer.

[fboehm]

@editorialbot assign @DanielRivasMD as reviewer

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[fboehm]

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[fboehm]

@editorialbot add @DanielRivasMD as reviewer

[editorialbot]

@DanielRivasMD added to the reviewers list!

[stmcg]

Thanks for the invitation. I’m unfortunately not available to review this submission as it caught me at a particularly busy time. Please keep me in mind for future submissions though.

Best, Sean

On Mar 17, 2022, at 7:54 AM, Frederick Boehm @.**@.>> wrote:

@JoranTiUhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_JoranTiU&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=jrca-6ijHBDY8AS_Bga5oj1A2gNlYQcGygnJe_xpNq0&m=2WF5z6d7HWicPBeevWWN8nx44rkBUNB-4sAKLCyJNmdzKimuvVYDNG_Vb8qmIgCU&s=wTz53B_gwELXjpewEwOXGmhh4NG6ucG-ITlHmYy-Nu4&e=, @stmcghttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_stmcg&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=jrca-6ijHBDY8AS_Bga5oj1A2gNlYQcGygnJe_xpNq0&m=2WF5z6d7HWicPBeevWWN8nx44rkBUNB-4sAKLCyJNmdzKimuvVYDNG_Vb8qmIgCU&s=B1JK0GQhQgOmN8FmzJ40wzWkjC5DfpNJZl_6Bno3HU8&e=, @DanielRivasMDhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_DanielRivasMD&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=jrca-6ijHBDY8AS_Bga5oj1A2gNlYQcGygnJe_xpNq0&m=2WF5z6d7HWicPBeevWWN8nx44rkBUNB-4sAKLCyJNmdzKimuvVYDNG_Vb8qmIgCU&s=O2GBtz_mD3ku4pGo2f1fvmLfmwYZ3uGOKFwTtx5dlq8&e=, @jaybee84https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jaybee84&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=jrca-6ijHBDY8AS_Bga5oj1A2gNlYQcGygnJe_xpNq0&m=2WF5z6d7HWicPBeevWWN8nx44rkBUNB-4sAKLCyJNmdzKimuvVYDNG_Vb8qmIgCU&s=hBh_avtJA45iGz5A6hRGUj3KYKfawnQKYk_a132jhpQ&e= - would any of you be willing to review this submission to JOSS? The review process at JOSS is unique: it takes place in a GitHub issue, is open, and author-reviewer-editor conversations are encouraged.

JOSS reviews involve downloading and installing the software, and inspecting the repository and submitted paper for key elements. See https://joss.readthedocs.io/en/latest/review_criteria.htmlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__joss.readthedocs.io_en_latest_review-5Fcriteria.html&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=jrca-6ijHBDY8AS_Bga5oj1A2gNlYQcGygnJe_xpNq0&m=2WF5z6d7HWicPBeevWWN8nx44rkBUNB-4sAKLCyJNmdzKimuvVYDNG_Vb8qmIgCU&s=4VMn5e6pMWkytT6myRK7g9TvbrdNikJGxHXA3wU0ctM&e=

Editors and reviewers post comments on the Review issue, and authors respond to the comments and improve their submission until acceptance (or withdrawal, if they feel unable to satisfy the review).

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[JoranTiU]

I can be a second reviewer on this 😊

[jaybee84]

I am happy to review this.

Thanks, Jineta

[fboehm]

Thanks so much, @JoranTiU, @jaybee84 and @stmcg ! @stmcg - I'll be certain to ask you again when you're less busy. @JoranTiU - I'll assign you as a second reviewer. @jaybee84 - I hope that we can work together on a future submission. I saw that @JoranTiU responded just before you, so I've assigned them as the second reviewer. We should need only two reviewers for this submission. Regardless, @jaybee84 - I really appreciate your willingness to help out, and I'll have to ask you to review a future submission. Thanks, everyone!

[fboehm]

@editorialbot add @JoranTiU as reviewer

[editorialbot]

@JoranTiU added to the reviewers list!

[fboehm]

@editorialbot begin review

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@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/4251.

[JoranTiU]

Hi all,

I can be the second reviewer on this 😊

Vriendelijke groet/Kind Regards, Joran

Joran Jongerling | Assistant-Professor | Department of Methodology and Statistics | Tilburg School of Social and Behavioral Sciences | Simon Building, room S706

Van: Daniel Rivas @.> Verzonden: donderdag 17 maart 2022 1:49 Aan: openjournals/joss-reviews @.> CC: Joran Jongerling @.>; Mention @.> Onderwerp: Re: [openjournals/joss-reviews] [PRE REVIEW]: rbmi: A R package for standard and reference-based multiple imputation methods (Issue #4224)

Sounds great! Let's do it! I read the article, and will install and test the software, is this the review thread where I should comment? Or where can I find it?

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/4224#issuecomment-1070887182, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVCJOPBRRSATZJMNFYWK6ZLVAMS37ANCNFSM5QADS2YQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.**@.>>

[fboehm]

@JoranTiU - Thank you so much for the offer! We've actually completed the review for this submission. I hope that you and I can work together on a future submission. Thanks again!

[JoranTiU]

I hope so too 😊. And you’re very welcome 😊

Vriendelijke groet/Kind Regards, Joran

Joran Jongerling | Assistant-Professor/Co-Director of TESC | Department of Methodology and Statistics | Tilburg School of Social and Behavioral Sciences | Reitse Poort, Room RP 15 | https://experiencesampling.nl/person/joran-jongerling/

@.***

From: Frederick Boehm @.> Sent: zondag 16 oktober 2022 4:38 To: openjournals/joss-reviews @.> Cc: Joran Jongerling @.>; Mention @.> Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: rbmi: A R package for standard and reference-based multiple imputation methods (Issue #4224)

@JoranTiUhttps://github.com/JoranTiU - Thank you so much for the offer! We've actually completed the review for this submission. I hope that you and I can work together on a future submission. Thanks again!

— Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/4224#issuecomment-1279982656, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVCJOPGTEB5ZEB2IRVPD243WDQHMNANCNFSM5QADS2YQ. You are receiving this because you were mentioned.Message ID: @.***>