What is literate progamming?

Let us change our traditional attitude to the construction of programs: Instead of imagining that our main task is to instruct a computer what to do, let us concentrate rather on explaining to human beings what we want a computer to do.

What is literate programming?

• Documentation containing code (not vice versa!)

• Direct connection between code and explanation

• Convey meaning to humans rather than telling computer what to do!

• Multiple “scales” possible

Why literate programming?

• Your analysis scripts are computer software

• Integrate math, figures, code, and narrative in one place

• Explaining something helps you learn it

Pseudocode and literate programming

• An informal way of writing the ‘logic’ of your program

• Balance between readability and precision

• Avoid syntactic drift

Writing pseudocode

What is Quarto?

• A multi-language platform for developing reproducible documents

• A ‘lab notebook’ for your analyses

• Allows transparent, reproducible scientific reports and presentations

Key components

1. Metadata and global options: YAML

2. Text, figures, and tables: Markdown and LaTeX

3. Code: knitr (or jupyter if you’re into that sort of thing)

YAML - Yet Another Markup Language

1. Allows you to set (or change) output format

2. Provide options that apply to the entire document

3. Spacing matters!

Formatting Text

• Basic formatting via Markdown

• Fancier options using Divs and spans via Pandoc

• Fenced Divs start and end with ::: (can be any number >3 but must match)

Adding Code Chunks

• Use 3x ``` on each end

• Include the engine {r} (or python or Julia)

• Include options beneath the “fence” using a hashpipe (#|)