editorialbot commented 9 months ago

Submitting author: !--author-handle-->@limengbinggz@Nikoleta-v3<!--end-editor-- Reviewers: @jamesuanhoro, @larryshamalama Archive: 10.5281/zenodo.12711232

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2cffa48f57384769d086069f824fd020"><img src="https://joss.theoj.org/papers/2cffa48f57384769d086069f824fd020/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2cffa48f57384769d086069f824fd020/status.svg)](https://joss.theoj.org/papers/2cffa48f57384769d086069f824fd020)

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

@jamesuanhoro & @larryshamalama, 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 @Nikoleta-v3 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 @larryshamalama

📝 Checklist for @jamesuanhoro

editorialbot commented 3 months ago

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

OK DOIs

- 10.18637/jss.v061.i13 is OK
- 10.18637/jss.v042.i10 is OK
- 10.1109/TPAMI.2014.2313115 is OK
- 10.1093/oso/9780198526155.003.0042 is OK
- 10.1080/03610918.2012.718840 is OK

MISSING DOIs

- No DOI given, and none found for title: randomLCA: An R package for latent class with rand...
- No DOI given, and none found for title: Tree-Regularized Bayesian Latent Class Analysis fo...
- No DOI given, and none found for title: Validating Bayesian inference algorithms with simu...

INVALID DOIs

- None

Nikoleta-v3 commented 3 months ago

@limengbinggz can you check if you can find DOIs for the above publications? ⬆️

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:

limengbinggz commented 3 months ago

I appreciate your advice on the vignettes. Could you please give me more specific suggestions about what can be added to the vignettes for improvement? Thank you!

The current vignette is really to accompany your paper. I was thinking of having vignettes for the different functionalities of the package. Are all the functionalities of ddtlcm being captured by the current vignette?

Thanks! I do think the current vignettes is to demonstrate all the functionalities of the package, basically data simulation, model estimation and inference, and visualization.

limengbinggz commented 3 months ago

@limengbinggz can you check if you can find DOIs for the above publications? ⬆️

I have updated the DOI for randomLCM. The other two references do not have DOIs so I am leaving them blank. Thanks!

Nikoleta-v3 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

- 10.18637/jss.v061.i13 is OK
- 10.18637/jss.v042.i10 is OK
- 10.18637/jss.v081.i13 is OK
- 10.1109/TPAMI.2014.2313115 is OK
- 10.1093/oso/9780198526155.003.0042 is OK
- 10.1080/03610918.2012.718840 is OK

MISSING DOIs

- No DOI given, and none found for title: Tree-Regularized Bayesian Latent Class Analysis fo...
- No DOI given, and none found for title: Validating Bayesian inference algorithms with simu...

INVALID DOIs

- None

Nikoleta-v3 commented 3 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

Nikoleta-v3 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

- 10.18637/jss.v061.i13 is OK
- 10.18637/jss.v042.i10 is OK
- 10.18637/jss.v081.i13 is OK
- 10.1109/TPAMI.2014.2313115 is OK
- 10.1093/oso/9780198526155.003.0042 is OK
- 10.1080/03610918.2012.718840 is OK

MISSING DOIs

- No DOI given, and none found for title: Tree-Regularized Bayesian Latent Class Analysis fo...
- No DOI given, and none found for title: Validating Bayesian inference algorithms with simu...

INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/dsais-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/5620, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon commented 3 months ago

🔍 checking out the following:

[x] reviewer checklists are completed or addressed
[x] version set
[x] archive set
[x] archive names (including order) and title in archive matches those specified in the paper
[x] archive uses the same license as the repo and is OSI approved as open source
[x] archive DOI and version match or redirect to those set by editor in review thread
[x] paper is error free - grammar and typos
[x] paper is error free - test links in the paper and bib
[x] paper is error free - refs preserve capitalization where necessary
[x] paper is error free - no invalid refs without justification

crvernon 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:

crvernon commented 3 months ago

:wave: @limengbinggz - Thanks for your work on this. We just need to clear one more thing before I can accept this for publication:

[ ] The license listed in your Zenodo archive should match the license listed for your software. Please edit the metadata of your Zenodo archive to make this so. No need to conduct a new release.

Let me know when this as done and we will move forward. Thanks!

limengbinggz commented 3 months ago

https://github.com/limengbinggz/ddtlcm

👋 @limengbinggz - Thanks for your work on this. We just need to clear one more thing before I can accept this for publication:

[x] The license listed in your Zenodo archive should match the license listed for your software. Please edit the metadata of your Zenodo archive to make this so. No need to conduct a new release.

Let me know when this as done and we will move forward. Thanks!

Thank you for the nudge! I have corrected my license on Zenodo.

crvernon commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 3 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Li given-names: Mengbing orcid: "https://orcid.org/0000-0002-2264-8006" - family-names: Wu given-names: Bolin - family-names: Stephenson given-names: Briana - family-names: Wu given-names: Zhenke orcid: "https://orcid.org/0000-0001-7582-669X" contact: - family-names: Li given-names: Mengbing orcid: "https://orcid.org/0000-0002-2264-8006" - family-names: Wu given-names: Zhenke orcid: "https://orcid.org/0000-0001-7582-669X" doi: 10.5281/zenodo.12711232 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Li given-names: Mengbing orcid: "https://orcid.org/0000-0002-2264-8006" - family-names: Wu given-names: Bolin - family-names: Stephenson given-names: Briana - family-names: Wu given-names: Zhenke orcid: "https://orcid.org/0000-0001-7582-669X" date-published: 2024-07-15 doi: 10.21105/joss.06220 issn: 2475-9066 issue: 99 journal: Journal of Open Source Software publisher: name: Open Journals start: 6220 title: "ddtlcm: An R package for overcoming weak separation in Bayesian latent class analysis via tree-regularization" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06220" volume: 9 title: "ddtlcm: An R package for overcoming weak separation in Bayesian latent class analysis via tree-regularization" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot commented 3 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 3 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5624
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06220
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon commented 3 months ago

🥳 Congratulations on your new publication @limengbinggz! Many thanks to @Nikoleta-v3 for editing and @jamesuanhoro and @larryshamalama for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot commented 3 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06220">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06220/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06220/status.svg
   :target: https://doi.org/10.21105/joss.06220

This is how it will look in your documentation:

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limengbinggz commented 3 months ago

🥳 Congratulations on your new publication @limengbinggz! Many thanks to @Nikoleta-v3 for editing and @jamesuanhoro and @larryshamalama for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

Thank you very much to the editors and reviewers for your time and hard work! I really appreciate you help!

openjournals / joss-reviews

[REVIEW]: ddtlcm: An R package for overcoming weak separation in Bayesian latent class analysis via tree-regularization #6220

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance