An R reproducibility toolkit for the practical researcher

Welcome

  • 🗓️ The course will be held online, from 9 am to 12 pm (Berlin time), October (28th-31st).
    • ⏳with pauses every hour!
  • 📚Materiales: everything lives here: http://reproducibility.rocks/
  • ❓Check points (how familiar are you with ___?)
  • 🏃Exercises:
    • Follow along
    • breakout rooms
  • 📑Homework + mini reprohack challenges (optional)

Day 1

  1. Introduction
  2. Project structure
  3. RMarkdown

https://the-turing-way.netlify.app/reproducible-research/reproducible-research.html

https://towardsdatascience.com/scientific-data-analysis-pipelines-and-reproducibility-75ff9df5b4c5

https://rviews.rstudio.com/2018/01/18/package-management-for-reproducible-r-code/

Examples

Good file names

  • data/raw/madrid-minimum_temperature.csv

  • scripts/02-compute-mean_temperature.R

  • analysis/01-madrid-minimum_temperature-descriptive_statistics.Rmd

Exercise

Come up with good file names and folders for (choose two)

  • a dataset of cats with columns for weight, length, tail length, fur colour(s), fur type and name.

  • a script that downloads data from Spotify.

  • a scripts that cleans up data.

  • a scripts that fits a linear discriminant model and saves it to a file.

  • the .Rds file in which that model is stored.

03:00

Do you use RStudio projects?

😯 What’s that?

👍 I’m familiar with them.

👏 I use them sometimes.

❤️ I use them all the time.

Choose an emoji from Reactions

Does RMarkdown documents sound familiar to you?

😯 I don’t have a clue.

👍 I’ve heard of it.

👏 I’ve used it

❤️ I use it all the time.

Choose an emoji from Reactions

Does YAML sound familiar to you?

😯 I don’t have a clue.

👍 I’ve heard of it.

👏 I can understand it.

❤️ I can write valid yaml most of the time.

Choose an emoji from Reactions

Does LaTeX sound familiar to you?

😯 I don’t have a clue.

👍 I’ve heard of it.

👏 I’ve used it, unfortunately.

❤️ I use it all the time, unfortunately.

Choose an emoji from Reactions

Preparations for day 2:

  1. Portable file paths with here
    • Install the here package.
  2. Using git and GitHub (setup instructions)
    • Install git
    • Create GitHub account
    • Configure your system to use RStudio with GitHub
  3. Creating a research compendium
    • Install the rrtools package.