Orderly Tutorial

MRC Centre for Global Infectious Disease Analysis

The reproducibility rant

Slide Deck

Who uses it?

• Developed since May 2017 for the Vaccine Impact Modelling Consortium
• Adopted by the MRC Centre and used in the 2018-2020 DRC Ebola responses
• Used in the COVID-19 response, especially within the “real time modelling” group
• Used within research groups (HIV, Malaria, possibly others?)

Historical notes

• orderly (version 1)
  • Created for Vaccine Impact Modelling Consortium and strongly focussed on reproducible research
  • Used YAML everywhere
  • Supported simple ways of working for a small centralised team
• orderly2 (soon to be orderly 2.0.0)
  • A complete rewrite taking the best ideas from version 1 and dropping many less useful bits
  • Easier to program against
  • No more YAML
  • Focusses on distributed collaborative analysis
  • Also available as a python package!

Situation report

• Open RStudio - is it installed?
• Check your R version - does it start with 4.4?
• Do you have git installed?
• Does your RStudio have a git button?
• Go to https://github.com - are you logged in?
• Go to https://github.com/settings/organizations - are you in mrc-ide?

Next steps

• On to getting started
• Back to the project root