Reproducible reporting

Reproducible reporting

• To create human-readable reports
• Transparency, reusability and reproducibility
• Debugging

Literate programming

Programming paradigm introduced by Donald Knuth (1984) in which a computer program is given as an explanation of its logic in a natural language, embedded with code chunks, from which compilable source code can be generated.
(Adapted from Wikipedia)

Reproducible notebooks

• We use Quarto for reproducible documentation.
• Next generation development of Rmarkdown
• Supported by RStudio

Demonstration

Exercises

From OMA online book, Chapter 1: Microbiome data science in Bioconductor

microbiome.github.io/OMA/docs/devel/pages/intro.html

• Exercise 2
• Exercise 3
• Exercise 4

References