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[PRE REVIEW]: dsBinVal: Conducting distributed ROC analysis and Calibration using DataSHIELD #4473

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editorialbot opened this issue Jun 14, 2022 · 29 comments
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[PRE REVIEW]: dsBinVal: Conducting distributed ROC analysis and Calibration using DataSHIELD #4473

editorialbot opened this issue Jun 14, 2022 · 29 comments
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@csoneson @patRyserWelch8 @brunomontezano
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pre-review R TeX Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials

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editorialbot commented Jun 14, 2022 •
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Submitting author: @schalkdaniel (Daniel Schalk)
Repository: https://github.com/difuture-lmu/dsBinVal
Branch with paper.md (empty if default branch):
Version: v1.0.1
Editor: @csoneson
Reviewers: @patRyserWelch8, @brunomontezano
Managing EiC: Arfon Smith

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status

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HTML: <a href="https://joss.theoj.org/papers/05f3c28b18afafee51848423fd5b0e99"><img src="https://joss.theoj.org/papers/05f3c28b18afafee51848423fd5b0e99/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/05f3c28b18afafee51848423fd5b0e99/status.svg)](https://joss.theoj.org/papers/05f3c28b18afafee51848423fd5b0e99)

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

The author's suggestion for the handling editor is @csoneson.

@schalkdaniel 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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The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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

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=0.03 s (1713.0 files/s, 125126.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               32            400            476           1362
Markdown                         5            107              0            369
YAML                             5             33             11            179
Rmd                              1             55             70             79
TeX                              1              6              0             67
-------------------------------------------------------------------------------
SUM:                            44            601            557           2056
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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

OK DOIs

- 10.1093/ije/dyu188 is OK
- 10.3414/ME17-02-0022 is OK
- 10.48550/ARXIV.2203.10828 is OK
- 10.1111/j.0006-341x.2000.00352.x is OK
- 10.1007/11681878_14 is OK
- 10.2307/2531595 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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Wordcount for paper.md is 649

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

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arfon commented Jun 14, 2022

Note for other editors, this is a re-submission of a previously-rejecting submission (#4287)

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arfon commented Jun 14, 2022

@editorialbot invite @csoneson as editor

👋 @csoneson – would you be able to edit this submission for JOSS?

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Invitation to edit this submission sent!

@Kevin-Mattheus-Moerman
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@editorialbot invite @csoneson as editor

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Invitation to edit this submission sent!

@Kevin-Mattheus-Moerman
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@csoneson can you help with this one?

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Sorry for the delay - I must have missed the first invite. This is a bit outside my expertise, but I can give it a go.

@schalkdaniel - could you give a brief summary of the differences compared to the previous submission of this work? Also, if you have suggestions for reviewers (e.g. from the list linked in the first post above), please mention them here.

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@editorialbot assign @csoneson as editor

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Assigned! @csoneson is now the editor

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@csoneson - Sure, the first idea we had was to have multiple R packages to evaluate a binary classification model in a distributed setting. Therefore, we had a package for ROC curve and AUC calculation, calibration curves and other metrics, and a package for basic stuff like distributing an R model to multiple DataSHIELD servers. The previous submission just covers the ROC curve and AUC calculation while this submission is a merge and update of the three packages. So it contains the functionality to evaluate statistical or predictive models in multiple ways instead of just calculating the ROC curve and the AUC.

I don't really have preferences for the reviewer. But, I picked three candidates from the linked list who seem active on GitHub and do have a machine learning / biostats / bioinformatics background:

  • zhiiiyang
  • jaybee84
  • brunomontezano

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@schalkdaniel - great, thanks for the summary!

👋🏻 @zhiiiyang, @brunomontezano - would you be interested in reviewing this submission for JOSS?

dsBinVal: Conducting distributed ROC analysis and Calibration using DataSHIELD

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@csoneson, I might not have time to review this one. Feel free to pass me.

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@zhiiiyang - no worries, thanks for letting us know!

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csoneson commented Jul 3, 2022

👋🏻 @gsfyrakis, @patRyserWelch8, @MaximLippeveld - would (two of) you be available and interested in reviewing this submission for JOSS?

dsBinVal: Conducting distributed ROC analysis and Calibration using DataSHIELD

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patRyserWelch8 commented Jul 4, 2022 via email

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csoneson commented Jul 4, 2022

@patRyserWelch8 Thank you! We usually ask reviewers to provide a first round of reviews within ~2 weeks (once we have secured two reviewers, I will assign you and open the review issue, where you will be able to generate your review checklist and start the review). However, I should also note that in many cases it is easier to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

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@schalkdaniel - great, thanks for the summary!

👋🏻 @zhiiiyang, @brunomontezano - would you be interested in reviewing this submission for JOSS?

dsBinVal: Conducting distributed ROC analysis and Calibration using DataSHIELD

Firstly, thanks for the invitation. And secondly, I accept the invite to review this paper.

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csoneson commented Jul 5, 2022

@brunomontezano - brilliant, thanks! As we now have our two reviewers, I will start the review issue.

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csoneson commented Jul 5, 2022

@editorialbot add @patRyserWelch8 as reviewer

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@patRyserWelch8 added to the reviewers list!

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csoneson commented Jul 5, 2022

@editorialbot add @brunomontezano as reviewer

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@brunomontezano added to the reviewers list!

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csoneson commented Jul 5, 2022

@editorialbot start review

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OK, I've started the review over in #4545.

@editorialbot editorialbot added the Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials label Sep 10, 2022
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@arfon @csoneson @zhiiiyang @Kevin-Mattheus-Moerman @schalkdaniel @patRyserWelch8 @brunomontezano @editorialbot