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[PRE REVIEW]: rbmi: A R package for standard and reference-based multiple imputation methods #4224

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editorialbot opened this issue Mar 5, 2022 · 42 comments
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[PRE REVIEW]: rbmi: A R package for standard and reference-based multiple imputation methods #4224

editorialbot opened this issue Mar 5, 2022 · 42 comments
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@fboehm @DanielRivasMD @JoranTiU
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C++ pre-review R Stan waitlisted Submissions in the JOSS backlog due to reduced service mode.

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editorialbot commented Mar 5, 2022 •
edited

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

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c23a2dbed03cd0c8a1e790de9b078a7a"><img src="https://joss.theoj.org/papers/c23a2dbed03cd0c8a1e790de9b078a7a/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c23a2dbed03cd0c8a1e790de9b078a7a/status.svg)](https://joss.theoj.org/papers/c23a2dbed03cd0c8a1e790de9b078a7a)

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Thanks for submitting your paper to JOSS @nociale. Currently, there isn't an JOSS editor assigned to your paper.

@nociale if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

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Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

⚠️ 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.

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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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
-------------------------------------------------------------------------------
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
JSON                             1              0              0             21
C/C++ Header                     1              0              1              0
-------------------------------------------------------------------------------
SUM:                            95           4616           4614          17816
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 940

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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

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

@Kevin-Mattheus-Moerman
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@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 ☝️ , 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 Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Mar 5, 2022
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@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
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kthyng commented Mar 15, 2022

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

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kthyng commented Mar 15, 2022

@editorialbot invite @fboehm as editor

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Invitation to edit this submission sent!

@fboehm
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fboehm commented Mar 16, 2022

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

Thank you!

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fboehm commented Mar 16, 2022

@editorialbot assign @fboehm as editor

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Assigned! @fboehm is now the editor

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fboehm commented Mar 17, 2022

@editorialbot list reviewers

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

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fboehm commented Mar 17, 2022

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

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fboehm commented Mar 17, 2022

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.

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fboehm commented Mar 17, 2022

To get a sense of the checklist items, please see this ongoing review: #4242

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fboehm commented Mar 17, 2022

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.

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

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fboehm commented Mar 17, 2022

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.

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fboehm commented Mar 17, 2022

@editorialbot assign @DanielRivasMD as reviewer

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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fboehm commented Mar 17, 2022

@editorialbot commands

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Hello @fboehm, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author or reviewer to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for archive
@editorialbot set 10.21105/zenodo.12345 as archive

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Open the review issue
@editorialbot start review

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fboehm commented Mar 17, 2022

@editorialbot add @DanielRivasMD as reviewer

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@DanielRivasMD added to the reviewers list!

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stmcg commented Mar 17, 2022 via email

@JoranTiU
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I can be a second reviewer on this 😊

@jaybee84
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I am happy to review this.

Thanks,
Jineta

@fboehm
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fboehm commented Mar 18, 2022

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!

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fboehm commented Mar 18, 2022

@editorialbot add @JoranTiU as reviewer

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@JoranTiU added to the reviewers list!

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fboehm commented Mar 18, 2022

@editorialbot begin review

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

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fboehm commented Mar 18, 2022

@editorialbot start review

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OK, I've started the review over in #4251.

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JoranTiU commented Oct 11, 2022 via email

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fboehm commented Oct 16, 2022

@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!

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JoranTiU commented Oct 17, 2022 via email

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