How to use {targets} for effective workflows in R

Joel Nitta

Carpentry@UiO

2023/06/08

https://www.joelnitta.com

Introductions: instructor

@joelnitta@fosstodon.org

https://joelnitta.com

• Associate Professor @ Chiba University

• Research interests: Ecology and evolution of ferns

• Hobbies: Running (after my 7YO!)

Photo: J-Y Meyer

Introductions, cont’d

• Name

• Affiliation

• What do you want to do with {targets} and/or R?

Outline of today’s workshop

• Introduction to {targets}

• Live coding

• Lunch break

• More live coding

• Bring Your Own Data (BYOD)

Setup

• Local: Install R, RStudio, and targets

• Cloud: Sign in to the Posit Cloud instance (requires account; free)

Collaborative notes

• https://hackmd.io/@joelnitta/Hy-J75aL3/edit

• Please add your name if you are comfortable doing so.

• Workshop staff will take notes, but feel free to add anything you like.

Code of Conduct

• By participating in this workshop, you agree to abide by the Carpentries Code of Conduct

About The Carpentries

• Software Carpentry (since 1998) is an open workshop series for researchers to teach each other best practices for research computing as a community

• The Carpentries includes also Data Carpentry and Library Carpentry

• This lesson is in-development (not an official workshop, yet)

Why {targets}?

To make your code more reproducible

What is reproducibility?

The ability for others (or your future self) to re-run your code and get the same results

• Not “yes” or “no”
• Reproducibility = mindset
• Many aspects
  • Computing environment
  • Data availability
  • Code automation

Workflows in R

• Which steps need to be run in what order?

R for Data Science https://r4ds.had.co.nz/

Workflows in R

• If one part of a workflow changes, how does it affect other parts?

• How much of it do we need to re-run?

What is {targets}?

• Automates workflow

• Only runs necessary steps

• Can run workflow steps in parallel (speeds up analysis)

• Provides proof that results are derived from code

Resources

• Github https://github.com/ropensci/targets

• Package website https://docs.ropensci.org/targets/

• User manual https://books.ropensci.org/targets/

• Targetopia https://wlandau.github.io/targetopia/

• {tarchetypes} website https://docs.ropensci.org/tarchetypes/

• Discussion board https://github.com/ropensci/targets/discussions

Live Coding

All lesson materials at https://joelnitta.github.io/targets-workshop/