Reproducible Manuscripts with Quarto - posit::conf(2023)

Presented by Mine Çetinkaya-Rundel
In this talk, we present a new capability in Quarto that provides a straightforward and user-friendly approach to creating truly reproducible manuscripts that are publication-ready for submission to popular journals. This new feature, Quarto manuscripts, includes the ability to produce a bundled output containing a standardized journal format, source documents, source computations, referenced resources, and execution information into a single bundle that is ingested into journal review and production processes. We'll demo how Quarto manuscripts work and how you can incorporate them into your current manuscript development process as well as touch on pain points in your current workflow that Quarto manuscripts help alleviate.
Presented at Posit Conference, between Sept 19-20 2023,
Learn more at posit.co/conference.
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Talk Track: Quarto (1).
Session Code: TALK-1070

[@pandumulyamuhammadsyah]

Thanks for the valuable information. It's really fascinating how writing research paper could be fun and enjoyable.

[@adriant1168]

Amazing

[@tangibleoxygen1986]

Awesome

[@damanrique]

That's an amazing approach. I have a question. As you are aware, we scientists do not generate single visualozations in our articles, like thr example shown. Instead, we work with pannels incorporating several figures and images organized in different ways. Is there a way quarto facilitates building those figure/images pannels? Thank you.

[@tamiresmartins1296]

you can create your plots using ggplot2 and join them with functions from the patchwork or cowplot packages, for exemple.

[@PositPBC]

Yes! Please check out the figures documentation on the Quarto site: quarto.org/docs/authoring/figures.html

[@haraldurkarlsson1147]

The problem I have run into with publications that supply the code and other data as supplements is that the code is frequently out of date and thus breaks when attempting to run it. Moreover, annotation is often lacking so it is hard to tell what the authors were doing. To boot the format of data may be poor. I have for instance come across papers where the supplementary data was stored in a bunch of word tables. I think there needs to be some sort of standard for both the code and data format set by the journals or reproducibility is just wishful thinking.