Quarto, the table 2 fallacy and more
1 - Quarto: the next generation of R Markdown
R Markdown is a tool that helps data scientists, researchers and data enthusiasts to code and produce beautiful reports at the same time. Quarto is the next generation of R Markdown with several built in features. What I found most amazing so far is the possibility to serve a notebook with shiny apps embedded on it! Check it out following the link below.
https://quarto.org/
I particularly started using quarto for the class I am teaching this semester to show the students some information and the results look very nice. You can check it out here:
https://chronchi.github.io/transcriptomics
This tool will be my go to when doing analysis and writing reports in the future. Let me know if you use it to publish a book using quarto or any quarto document embedded with shiny apps. I'm looking for examples!
PS: Quarto means fourth and room in portuguese (and other latin languages probably), hence their symbol, a circle sliced in four parts.
2 - The table 2 fallacy
When calculating odds and hazard ratios one adjusts for several confounders usually. The problem is that the interpration of the confounders is not quite the same as the main effect. The paper belows discuss the interpration of the confounder effects, the so called table 2 fallacy.
https://academic.oup.com/aje/article/177/4/292/147738?login=false
Richard McElreath in his lecture 04 shows how to use bayesian inference to interpret these results under the framework of DAGs, a causal inference tool. I highly recommend checking his videos, in particular the lecture 04:
https://www.youtube.com/watch?v=QiHKdvAbYII
3 - Getting rid of scientific papers?
With the advent of public repositories, should we simply ditch the publication process? The article below discuss several problems of the current publishing process and gives us food for thought regarding this question.
https://www.theguardian.com/books/2022/apr/11/the-big-idea-should-we-get-rid-of-the-scientific-paper
4 - Regression and other stories
Regression and other stories is a book by Andrew Gelman, Jennifer Hill and Aki Vehtari. They go over the basics of linear regression, statistics and show how to use and interpret linear models with several real life examples. This book is a great introduction to general linear regression under the bayes perspective. A link to the freely available pdf can be found below.
https://avehtari.github.io/ROS-Examples/