orderly Tutorial

A site for orderly training; you may prefer to go to the actual site if you want the content.

Development

You will need to install quarto, start here to do so.

You will also need a very recent version of orderly, the easiest way is probably

install.packages(
  "orderly",
  repos = c("https://mrc-ide.r-universe.dev", "https://cloud.r-project.org"))

Run

quarto preview

which will open the site in a browser. Then edit the .qmd pages; changes will rebuild automatically.

The site will build when pushed to GitHub, so failures will show on a PR. It will push to gh-pages automatically when merged.

Documentation for quarto is here and for revealjs presentations specifically here

Quirks that I have bashed into this attempt:

Links between parts of the site:

• From a non-slide .qmd you can use whatever.qmd as a target and it will work fine
• From the slides this won't work, and I can't find a good reason why or discussion of a workaround. Include a manual link to the final rendered version.

Data sources

Data sources

• inputs/part2/wuenic.xlsx comes from the WHO
• inputs/part2/data.xlsx is entirely synthetic
• inputs/part3/cases.csv.xz from Rawson et al. (2024) and associated orderly1 project