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[PRE REVIEW]: Deident: An R package for data anonymization 1 #7078

Closed editorialbot closed 2 months ago

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@Stat-Cook<!--end-author-handle-- (Robert Cook) Repository: https://github.com/Stat-Cook/deident Branch with paper.md (empty if default branch): Version: V1.0 Editor: !--editor-->@spholmes<!--end-editor-- Reviewers: @PatrickRWright, @nrennie Managing EiC: Chris Vernon

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Markdown: [![status](https://joss.theoj.org/papers/8f0aeec3b02966a6f7f527283b6c150a/status.svg)](https://joss.theoj.org/papers/8f0aeec3b02966a6f7f527283b6c150a)

Author instructions

Thanks for submitting your paper to JOSS @Stat-Cook. Currently, there isn't a JOSS editor assigned to your paper.

@Stat-Cook if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

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:

@editorialbot commands
editorialbot commented 3 months ago

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:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf
editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.05 s (2355.7 files/s, 254249.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            45           1340            155           6273
R                               55            623           1006           1731
CSS                              3             98             52            442
XML                              2              0              0            292
JavaScript                       3             64             32            256
CSV                              2              0              0            202
Markdown                         3             53              0            185
TeX                              2             14              0            112
YAML                             5              2              4             71
Rmd                              4            141            287             44
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           125           2335           1537           9619
-------------------------------------------------------------------------------

Commit count by author:

    81  Rob
    17  Robert Cook
editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 1060

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

🟡 License found: Other (Check here for OSI approval)

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf. Problem with ORCID (0000-0000-0000-0000) for Robert Cook. Invalid ORCID.

crvernon commented 3 months ago

:wave: @Stat-Cook - while I am getting you an editor assigned, could you correct the ORICD that is causing the paper compile issue above? Thanks.

crvernon commented 3 months ago

@editorialbot invite @adi3 as editor

👋 @adi3 - can you take this one on as editor?

editorialbot commented 3 months ago

Invitation to edit this submission sent!

Stat-Cook commented 3 months ago

@crvernon Hopefully thats sorted the ORCID issue.

crvernon commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf. Problem with ORCID (0000-0000-0000-0000) for Md Asaduzaman. Invalid ORCID.

crvernon commented 3 months ago

@Stat-Cook same issue with the above.

Stat-Cook 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:

editorialbot commented 3 months ago

Five most similar historical JOSS papers:

BIDSonym: a BIDS App for the pseudo-anonymization of neuroimaging datasets Submitting author: @peerherholz Handling editor: @oliviaguest (Active) Reviewers: @deep-introspection, @chrisgorgo, @neuromusic Similarity score: 0.7109

DeGAUSS: Decentralized Geomarker Assessment for Multi-Site Studies Submitting author: @cole-brokamp Handling editor: @pjotrp (Retired) Reviewers: @vsoch, @george-githinji Similarity score: 0.6966

dataquieR: assessment of data quality in epidemiological research Submitting author: @ Handling editor: @csoneson (Active) Reviewers: @borishejblum, @cmirzayi Similarity score: 0.6786

Web-based text anonymization with Node.js: Introducing NETANOS (Named entity-based Text Anonymization for Open Science) Submitting author: @ben-aaron188 Handling editor: @acabunoc (Retired) Reviewers: @RichardLitt Similarity score: 0.6771

secuTrialR: Seamless interaction with clinical trial databases in R Submitting author: @PatrickRWright Handling editor: @csoneson (Active) Reviewers: @pacoramon, @sachsmc Similarity score: 0.6714

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

Stat-Cook commented 3 months ago

@crvernon I think thats the ORCID issue fixed. Anything else I need to do?

crvernon commented 3 months ago

Thanks @Stat-Cook. Just waiting to get you a topic editor assigned. All good for now. Thanks!

crvernon commented 3 months ago

@editorialbot invite @JBorrow as editor

:wave: @JBorrow since we are wrapping up one of your other submissions, do you think you can take this one on?

editorialbot commented 3 months ago

Invitation to edit this submission sent!

JBorrow commented 3 months ago

@crvernon unfortunately I don't have any R experience, and my community doesn't use it, so I would not be the best choice to edit this package. I would be happy to take on a different package in different language, though (python, C, golang, fortran, javascript, ...)

crvernon commented 3 months ago

No problem @JBorrow, thanks!

crvernon commented 3 months ago

@editorialbot invite @RMeli as editor

:wave: @RMeli can you edit this one?

editorialbot commented 3 months ago

Invitation to edit this submission sent!

RMeli commented 3 months ago

@crvernon I also have no experience with R at all, and I'll soon go on holidays so I think it would be better to find another editor. But please let me know if you can't find anyone and I'll step in when I'll be back from holidays.

crvernon commented 2 months ago

Thanks for the notice @RMeli

crvernon commented 2 months ago

@editorialbot invite @spholmes as editor

:wave: @spholmes - can you take this one on as editor?

editorialbot commented 2 months ago

Invitation to edit this submission sent!

spholmes commented 2 months ago

@editorialbot invite @spholmes as editor

👋 @spholmes - can you take this one on as editor?

Yes I can...

crvernon commented 2 months ago

@editorialbot assign @spholmes as editor

Thanks @spholmes!

editorialbot commented 2 months ago

Assigned! @spholmes is now the editor

spholmes commented 2 months ago

Hi @PatrickRWright Would you be able to review this JOSS submission for us? Many Thanks Susan

spholmes commented 2 months ago

Hello @peerherholz As an author of a paper on data in JOSS, we thought you might be able to help us out with a review of this submission on the R package Deident. Would you be able to help us out here? Thanks Susan

PatrickRWright commented 2 months ago

What are the responsibilities and what is the timeline?

I can really only make technical comments even though I understand, and agree with the general need for such methods. Off the top of my head I was wondering if it may be possible to show the code coverage badge for the package and why the authors decided not to submit to CRAN.

spholmes commented 2 months ago

What are the responsibilities and what is the timeline?

I can really only make technical comments even though I understand, and agree with the general need for such methods. Off the top of my head I was wondering if it may be possible to show the code coverage badge for the package and why the authors decided not to submit to CRAN.

Thanks @PatrickRWright , it is valid to ask the CRAN question and there is a quick checklist the reviewers go trhough, it is public on the github review issue, as was the one for your paper: https://github.com/openjournals/joss-reviews/issues/2816

We like to get finished with the review after a few weeks if possible, the authors respond to the questions as they come up. The code is available and statistics for the code coverage and type are automatically generated byt the github bot.

Let me know if you have other questions, and thanks fore your prompt reply. Susan

PatrickRWright commented 2 months ago
  1. DESCRIPTION file needs to be adjusted with actual information. It still contains placeholder info.
  2. babyname_sample.rda has no trace. i.e. how was it produced? Also it seems to be potentially unused. Maybe its better removed from the package? --> I will not install a package from GItHub with an rda for which I can't find a clear trace.
  3. I suggest adding a NEWS.md file to be able to track a sensible changelog.

All above are basic checks for R Packages. I thus suggest going over best practices here https://r-pkgs.org/.

Stat-Cook commented 2 months ago

@PatrickRWright thanks for the quick notes.

  1. Fixed - sorry overlooked updating this.
  2. Thanks for noticing this, old version of examples/ vignettes used this file. The file and all references in documentation have been removed.
  3. NEWS.md has been added.

Currently re-reviewing the package practices but please say if anything else comes to mind.

spholmes commented 2 months ago

@editorialbot add @PatrickRWright as reviewer

editorialbot commented 2 months ago

@PatrickRWright added to the reviewers list!

spholmes commented 2 months ago

@PatrickRWright : All these comments are useful but we usually create a new thread for reviews and this is done through the editorialbot. There will be a new issue created and then you can see your checklist

spholmes commented 2 months ago

@editorialbot start review

editorialbot commented 2 months ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7157.

spholmes commented 2 months ago

@Stat-Cook : We have started a new thread with the reviewing issue https://github.com/openjournals/joss-reviews/issues/7157.

spholmes commented 2 months ago

Hi @nrennie, I wonder if you are interested in helping us review this submission to JOSS?

PeerHerholz commented 2 months ago

Hello @PeerHerholz As an author of a paper on data in JOSS, we thought you might be able to help us out with a review of this submission on the R package Deident. Would you be able to help us out here? Thanks Susan

Hi @spholmes and everyone,

I totally missed this, I'm very sorry. It sounds super interesting but I'm not that familiar with R and especially the development/publishing aspects. Thus, I can't be that helpful here. I hope you'll find a fitting reviewer soon.

Sorry again.

Best, Peer

nrennie commented 2 months ago

Hi @nrennie, I wonder if you are interested in helping us review this submission to JOSS?

Yes, I'd be happy to review it

spholmes commented 2 months ago

@editorialbot add @nrennie as reviewer

editorialbot commented 2 months ago

@nrennie added to the reviewers list!

spholmes commented 2 months ago

@nrennie : Many Thanks You'll see a new review issue here : https://github.com/openjournals/joss-reviews/issues/7157 please generate your checklist there with the editorialbot by asking it: @editorialbot generate my checklist over there on the review issue.