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steno-aarhus / legliv

Substitution of red meat with legumes and risk of primary liver cancer in UK Biobank participants: A prospective cohort study
MIT License
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Submit the paper to bioRxiv (or Zenodo) as a preprint before or at the same time as uploading to Nutrients #19

Closed lwjohnst86 closed 2 months ago

lwjohnst86 commented 3 months ago

As per the purpose of the Steno UK Biobank project, we want our output to be put in archives as preprints.

nielsbock commented 3 months ago

Is this pretty straghtforward? I register an account on Zenodo and upload a pdf document with my paper? Or are there any guidelines I should follow?

lwjohnst86 commented 3 months ago

Yea, I don't know which would be better to do, but if you want to go the Zenodo route, I have already made a function for that in ukbAid. So I can do that for you, since I have an account already set up, along with tokens to use the function.

nielsbock commented 3 months ago

I've rebuild report.Rmd trying to mimic the quarto format you built for the protocol because I'm not allowed to upload a preprint with MDPI/Nutrients template. It's not complete yet, but do you think you can upload it to Zenodo tomorrow when I submit the article?

nielsbock commented 3 months ago

We have submitted the manuscript now! I am almost done with the preparations for the preprint

lwjohnst86 commented 3 months ago

👍🏻 No worries, I don't have time to look at UKB stuff today, but I can finish up your preprint prep and upload to Zenodo on Monday next week 😁 Congrats!!!! 🎉

lwjohnst86 commented 3 months ago

@nielsbock just to confirm, I should upload the report.pdf file right?

lwjohnst86 commented 3 months ago

And what about the supplemental text? I see it in the report.Rmd but not in the pdf. It needs to be regenerated I assume?

nielsbock commented 3 months ago

It's the report.pdf, yes. Supplemental tables and figure are in the pdf, just before references. I couldn't find a pandoc template putting supplemental materials after references.

nielsbock commented 3 months ago

@lwjohnst86 targets::tar_make() will now prepare all code needed to compile report.Rmd!

lwjohnst86 commented 2 months ago

Preprint is up! https://zenodo.org/records/12666778 DOI: https://doi.org/10.5281/zenodo.12666778