[REVIEW]: Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics in R

[editorialbot]

Submitting author: !--author-handle-->@bernadette-eu<!--end-author-handle-- (Lampros Bouranis) Repository: https://github.com/bernadette-eu/Bernadette Branch with paper.md (empty if default branch): Version: v1.1.5 Editor: !--editor-->@samhforbes<!--end-editor-- Reviewers: @rowlandseymour, @strengejacke Archive: 10.5281/zenodo.8376673

Status

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HTML: <a href="https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea"><img src="https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea/status.svg)](https://joss.theoj.org/papers/8ee5ffed37ccbd0a8de519553da6ceea)

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

@rowlandseymour & @strengejacke, 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 @samhforbes 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 @rowlandseymour

📝 Checklist for @strengejacke

[samhforbes]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.48550/arXiv.2211.15229 is OK
- 10.18637/jss.v076.i01 is OK
- 10.1093/aje/kwt133 is OK
- 10.1371/journal.pcbi.1008409 is OK
- 10.1007/s11222-016-9696-4 is OK
- 10.1038/s41467-021-21237-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "ref-carpenter2017stan"
IDREFS attribute rid references an unknown ID "ref-gostic"
IDREFS attribute rid references an unknown ID "ref-ward_react2"
IDREFS attribute rid references an unknown ID "ref-epiestim"
IDREFS attribute rid references an unknown ID "ref-rstan"
IDREFS attribute rid references an unknown ID "ref-brooks"
IDREFS attribute rid references an unknown ID "ref-Cori2013"
IDREFS attribute rid references an unknown ID "ref-bernadette"
IDREFS attribute rid references an unknown ID "ref-epidemia"
IDREFS attribute rid references an unknown ID "ref-psisloo2"
IDREFS attribute rid references an unknown ID "ref-bouranis"
IDREFS attribute rid references an unknown ID "ref-rsoft"

[samhforbes]

Hi @bernadette-eu I can see under the hood I think the citations aren't formatted in typical md style as JOSS needs it. See https://joss.readthedocs.io/en/latest/submitting.html section on citation.

[bernadette-eu]

Good morning @samhforbes, looking into it now.

[bernadette-eu]

@editorialbot generate pdf

[editorialbot]

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

[bernadette-eu]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.48550/arXiv.2211.15229 is OK
- 10.18637/jss.v076.i01 is OK
- 10.1093/aje/kwt133 is OK
- 10.1371/journal.pcbi.1008409 is OK
- 10.1007/s11222-016-9696-4 is OK
- 10.1038/s41467-021-21237-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[bernadette-eu]

@samhforbes When rendering my paper.rmd file to paper.md, the references would be indicated by #ref-.... I manually updated the paper.md file, hopefully there will be no issues when creating the metadata file next time.

Please proceed and let me know if anything comes up.

Thanks.

[samhforbes]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.48550/arXiv.2211.15229 is OK
- 10.18637/jss.v076.i01 is OK
- 10.1093/aje/kwt133 is OK
- 10.1371/journal.pcbi.1008409 is OK
- 10.1007/s11222-016-9696-4 is OK
- 10.1038/s41467-021-21237-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/sbcs-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/4611, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[bernadette-eu]

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

@samhforbes looking at the final proof, the references in for Carpenter and Cori have not been updated. But the respective references in the intermediate proof looks fine. The rest of the document looks good.

[samhforbes]

Hi @bernadette-eu in the final link from editorial bot these look right to me, or am I missing something? I see volumes and DOIs

[bernadette-eu]

Hi @bernadette-eu in the final link from editorial bot these look right to me, or am I missing something? I see volumes and DOIs

Apparently I was looking at a preview download... My apologies. Checked again, everything looks good!

[samhforbes]

Awesome, I'll leave this to @openjournals/sbcs-eics then! Well done on a great package.

[arfon]

@bernadette-eu – could you please merge this tiny PR? https://github.com/bernadette-eu/Bernadette/pull/14

[bernadette-eu]

@bernadette-eu – could you please merge this tiny PR? bernadette-eu/Bernadette#14

Done!

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Bouranis given-names: Lampros orcid: "https://orcid.org/0000-0002-1291-2192" doi: 10.5281/zenodo.8376673 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Bouranis given-names: Lampros orcid: "https://orcid.org/0000-0002-1291-2192" date-published: 2023-09-26 doi: 10.21105/joss.05612 issn: 2475-9066 issue: 89 journal: Journal of Open Source Software publisher: name: Open Journals start: 5612 title: "Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics in R" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05612" volume: 8 title: "Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics in R" ```

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4615
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05612
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[bernadette-eu]

@arfon https://joss.theoj.org/papers/10.21105/joss.05612 does not contain the final pdf yet. Regarding closing this review issue, is this something I should do? Cannot seem to find the related button for this.

[arfon]

Looks like GitHub Pages is having a few issues. We'll leave this issue open until it resolves (may be a few hours)

[bernadette-eu]

@arfon The problem with GitHub pages has been resolved, so maybe the issue can close.

@samhforbes @rowlandseymour @strengejacke Thank you all for the smooth reviewing process!

Lampros Bouranis

[arfon]

Yep, looks like it's working now!

@rowlandseymour, @strengejacke – many thanks for your reviews here and to @samhforbes for editing this submission! JOSS relies upon the volunteer effort of people like you and we simply wouldn't be able to do this without you ✨

@bernadette-eu – your paper is now accepted and published in JOSS :zap::rocket::boom:

[editorialbot]

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05612/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05612/status.svg
   :target: https://doi.org/10.21105/joss.05612

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