Welcome to the Advanced R3 course!

  • ✔️ Go to your assigned table
  • ✔️ Introduce yourselves to your table mates
  • ✔️ Open your AdvancedR3.Rproj RStudio project
  • ✔️ Just in case, do r3::install_packages_advanced()

Motivation for this course

Largely from desire for more effective and actual collaboration

Very low reproducibility in most of science (1)

From searching PubMed Central for all articles with search term: “(ipynb OR jupyter OR ipython) AND github”

Researchers don’t know how to collaborate effectively

We don’t get training in it, nor do we get much practice in it

Academia doesn’t encourage building and improving effective collaboration

Little published work on how to effectively collaborate

An example (2): Research group tries to work on improving their collaboration

  • Decide on tools and practices that are best for the group
  • Use “data partners” to co-work/co-code together

One direct way to collaborate is working on shared code for a project

Because by collaborating, you will also read others’ code.

Reading others’ code is necessary to improve as an experienced coder

  • You aren’t reading others’ code if:

    • you don’t collaborate with others directly on their code
    • you aren’t doing code reviews with colleagues
    • researcher’s don’t share their code
  • If we all aren’t reading others’ code, we all aren’t improving

Goal of course: Create and nurture a culture of openness through training

Course details

Setup and layout

  • Course is mix of:
    • “Code-alongs” (we type and explain, you type along)
    • Hands-on coding, discussing, and reading exercises
    • A group project at the end
  • All material is online (and openly licensed)
  • Less about coding, more about connecting with others
    • Draw table name from bowl each morning
    • Introduce yourself to those at your table
    • During lunch, sit beside someone you don’t know
    • Several networking activities (usually after lunch)
  • Warning: You will be making a lot of functions!

Getting or asking for help 🙋‍♀️

  • Put the sticky (a.k.a. tiny paper hat 🎩) on your laptop to get help
  • There are lots of helpers
  • Table mates, help out too
  • We’re all learning here!
  • This is a supportive and safe environment
  • Remember our Code of Conduct

Practice using stickies/paper hats: Did you complete the checklist from the beginning?

Activities

🚶‍♀️🚶‍♂️ How do you perceive your skill in R?

🙋‍♀️ Who has had formal training in specifically coding in R or in general?

🚶‍♀️🚶‍♂️ Have you attended at least one of these courses before?

🚶‍♀️🚶‍♂️ If code for a paper was audited, how confident are you that the results could be reproduced exactly?

🚶‍♀️🚶‍♂️ How many of you work mostly on your own in your project(s)?

🚶‍♀️🚶‍♂️ How easy is it to collaborate with others on your project(s)?

🚶‍♀️🚶‍♂️ How many of you want to work more closely or collaboratively with others?

Alright, return to your seats! 🪑

1.
Samuel S, Mietchen D. Computational reproducibility of jupyter notebooks from biomedical publications. GigaScience. 2024;13.
2.
Turoman N, Hautekiet C, Jeanneret S, Valentini B, Langerock N. Open and reproducible practices in developmental psychology research: The workflow of the WomCogDev lab as an example. 2022 May;