[REVIEW]: surtvep: An R package for estimating time-varying effects

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@LingfengLuo0510@osorensen<!--end-editor-- Reviewers: @adibender, @turgeonmaxime Archive: 10.5281/zenodo.12575049

Status

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Markdown: [![status](https://joss.theoj.org/papers/cfccdf9c4b2e69546eafb629fc48dacb/status.svg)](https://joss.theoj.org/papers/cfccdf9c4b2e69546eafb629fc48dacb)

Reviewers and authors:

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@editorialbot generate my checklist

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crvernon commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 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 4 months ago

@editorialbot check references

editorialbot commented 4 months ago

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

OK DOIs

- 10.1051/0004-6361/201322068 is OK
- 10.1002/cncr.33174 is OK
- 10.1214/aos/1176347503 is OK
- 10.1111/j.2517-6161.1993.tb01939.x is OK
- 10.2307/2290630 is OK
- 10.1007/s10985-021-09544-2 is OK
- 10.1007/s11222-016-9666-x is OK
- 10.1007/978-1-4612-0919-5_38 is OK
- 10.1214/ss/1038425655 is OK
- 10.1016/j.cmpb.2005.11.006 is OK
- 10.1177/09622802231181471 is OK
- 10.2307/2532779 is OK
- 10.2307/2529620 is OK
- 10.1080/10618600.2016.1237364 is OK
- 10.1111/biom.13473 is OK

MISSING DOIs

- No DOI given, and none found for title: Using time dependent covariates and time dependent...
- No DOI given, and none found for title: A Package for Survival Analysis in R
- No DOI given, and none found for title: Generalized Additive Models: An Introduction with ...
- No DOI given, and none found for title: Surveillance, Epidemiology, and End Results (SEER)...
- No DOI given, and none found for title: Distribution of an information statistic and the c...

INVALID DOIs

- None

crvernon commented 4 months ago

:wave: @LingfengLuo0510 - thanks for all of your hard work on this. Your paper is very clean and that is much appreciated! I just need you to address a few final things before we accept this for publication:

[ ] Please edit the metadata in your Zenodo archive to make the license match what you use in your repository. Currently your license in the archive is specified as Creative Commons Attribution 4.0 International.
[ ] Please match the author order in your Zenodo archive to what is in your paper.

Let me know when these are done and I will move to accept.

LingfengLuo0510 commented 4 months ago

👋 @LingfengLuo0510 - thanks for all of your hard work on this. Your paper is very clean and that is much appreciated! I just need you to address a few final things before we accept this for publication:

[ ] Please edit the metadata in your Zenodo archive to make the license match what you use in your repository. Currently your license in the archive is specified as Creative Commons Attribution 4.0 International.

[ ] Please match the author order in your Zenodo archive to what is in your paper.

Let me know when these are done and I will move to accept.

@crvernon

Thanks a lot! (1) I have updated the license. It matches what I use in my repository. (2) I have adjusted the auther order. It matches the author order now.

Thanks again!

crvernon commented 4 months ago

@editorialbot accept

editorialbot commented 4 months ago

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

editorialbot commented 4 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: Luo given-names: Lingfeng - family-names: Wu given-names: Wenbo - family-names: Taylor given-names: Jeremy - family-names: Kang given-names: Jian - family-names: Kleinsasser given-names: Michael - family-names: He given-names: Kevin contact: - family-names: He given-names: Kevin doi: 10.5281/zenodo.12575049 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Luo given-names: Lingfeng - family-names: Wu given-names: Wenbo - family-names: Taylor given-names: Jeremy - family-names: Kang given-names: Jian - family-names: Kleinsasser given-names: Michael - family-names: He given-names: Kevin date-published: 2024-06-28 doi: 10.21105/joss.05688 issn: 2475-9066 issue: 98 journal: Journal of Open Source Software publisher: name: Open Journals start: 5688 title: "surtvep: An R package for estimating time-varying effects" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05688" volume: 9 title: "surtvep: An R package for estimating time-varying effects" ```

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 4 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 4 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/5550
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05688
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 4 months ago

🥳 Congratulations on your new publication @LingfengLuo0510! Many thanks to @osorensen for editing and @adibender and @turgeonmaxime 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 4 months ago

: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:

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HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05688">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05688/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05688/status.svg
   :target: https://doi.org/10.21105/joss.05688

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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LingfengLuo0510 commented 4 months ago

@crvernon I feel so sorry that may I ask if I can update the middle name of one of the authors? So sorry about this.

crvernon commented 4 months ago

Yes please do so. I am getting ready to board a flight but will reaccept this as soon as I can. Just let me know once you have made the change.

LingfengLuo0510 commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

:warning: An error happened when generating the pdf.

LingfengLuo0510 commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

:warning: An error happened when generating the pdf.

LingfengLuo0510 commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

:warning: An error happened when generating the pdf.

LingfengLuo0510 commented 4 months ago

Yes please do so. I am getting ready to board a flight but will reaccept this as soon as I can. Just let me know once you have made the change.

@crvernon Than Thanks a lot! I just updated the paper.md file (1) Jeremy Taylor -> Jeremy M.G. Taylor (2) Michael Kleinsasser -> Michael J. Kleinsasser

However, I'm encountering errors when generating the PDF, even after reverting to the previously accepted version. Could this be related to the paper's accepted status?

crvernon commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

:warning: An error happened when generating the pdf.

crvernon commented 4 months ago

@editorialbot reaccept

editorialbot commented 4 months ago

Rebuilding paper!

editorialbot commented 4 months ago

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/5551

crvernon commented 4 months ago

@LingfengLuo0510 - the paper should now reflect your changes.

editorialbot commented 4 months ago

: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:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05688/status.svg)](https://doi.org/10.21105/joss.05688)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05688">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05688/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05688/status.svg
   :target: https://doi.org/10.21105/joss.05688

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

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