Dad Joke

I got arrested today for walking out of an art museum with a painting.

I’m just so confused because when I asked the security if I could take a picture they said “yes”.

LaTeX

• Document preparation language and software
• Separates content from presentation

Pros

• Ideally, can quickly change the entire vibe of a document
• Amazing for citations
• “Smart” - makes things look beautiful

Cons

• Learning curve (better with Overleaf!)
• It’s a programming language - there can be bugs and exceptions
• Co-authors have to also use it

Markdown / R Markdown / Quarto

• Growing movement to build tools that output LaTeX using markdown that is easier to learn and work with
• Lots of promise here, but not quite as powerful

Knitr

• Very cool idea to put pointers to data directly in a LaTeX or Markdown document
• Can reference things (e.g., \(\beta\), SD, \(N\))
• Can even build figures
• In practice, I’ve found building figures earlier to work better

Workflow Management

• Eliminate, automate, or document!
• A number of tools for automating workflows
• Snakemake is fairly simple and Python-based

Snakemake

• Process for actually running all of the code needed to produce figures / papers
• Builds a Directed Acyclical Graph (DAG) of what needs to be done
• Only runs the parts where something has changed “upstream”
• Con is that you need to install more software

Discussion

Snakemake co-working