SCRUG: Using Markdown and Quarto to make reproducible reports

Emily Markowitz and Megsie Siple

2023-09-26

Quarto and Markdown

Quarto and Markdown enable you to weave together content and executable code into a finished product.

These slides were also made with Quarto.

More Quarto

The Quarto.org page has some solid “starting out” material

The rainbow of reproducible options 🌈

Low investment

• One-pagers
• Drafts of reports (layout and indexing are done, but more edits needed to publish)

Features

Data are accessible, minimal wrangling needed. Minimal hierarchy and repeats.

High investment

• Fully automated reports
• Very carefully formatted things

Features

• Parent and child docs, conditional situations, and special formatting.

Demo: A one-pager on snailfish

Clone the repo at https://github.com/scruglife/automated-reports-2023/.

Components

code/parent.qmd is a main reproducible doc. It is capable of having “child” docs referenced within, or it can exist as a standalone.

code/child_intro.R is a “child” document that inherits aesthetics and parameter values from parent.qmd

More stuff

How to use parameters in reports

Resources

• Eli Holmes repos and videos
• Tom Mock’s introduction (he starts with parameterizing!)

Examples from your peers

It can be helpful to see quarto and rmarkdown in practice. There are many reports being created by our colleges who post their code on GitHub.

• Easy: Bering Sea ADFG Activities Report by Nicole Charriere and Rebecca Haehn
• Moderate: Observer credible length ranges report by Chris Anderson
• Moderate: Special project posters and listings by Liz Dawson and Em Markowitz
• Very complicated: Bering Sea Data Report by Em Markowitz, Liz Dawson, and Chris Anderson
• Very very complicated: GAP Products documentation quarto book by many