Intro to EPI 590R

Why this class?

About this class

Goal: Learn some best practices to make your life in R easier and your research more reproducible

  • Quick! Intense!
    • It will require practice afterward, and time to sink in
    • The goal is to set you up for success and give you resources to learn more
  • You don’t have to use everything you learn here!
    • Some of these tools I use for every project, some just occasionally
    • Experiment with what works for you, a little at a time

About this class

  • Everything you need is at http://epi590r-2023.louisahsmith.com
    • Canvas will link you there, but good to bookmark as well
    • The website will be up indefinitely
  • General format:
    • Some overview slides
    • I’ll demonstrate while you watch
    • Practice on your own/with your classmates

Balance

About Louisa

  • Assistant professor at Northeastern University
    • Department of Health Sciences and the Roux Institute (Portland, Maine)
  • Started using R during my master’s (so almost 9 years of experience)
    • I learned mostly by doing!
    • Twitter, blogs, RStudio::conf videos, meetups
  • Basically everything I do is in R!
  • Actual epi research in causal inference, pregnancy, lots of other stuff

Most important thing about me

Why this class?

Errors are everywhere

No one and no field is immune from errors in data analysis. Our goal is to make them as unlikely as possible (and report them when we find them!)

But also!

  • It’s really boring to copy lots of numbers into a table
    • And then change a tiny thing in the analysis and do it all over again
  • It’s really frustrating to lose work when your computer crashes, or completely change an analysis before your advisor forgets what they told you last time and has you change it back
  • It’s fun when things just work! And you get more time for the fun parts of epidemiology

Questions?

Exercises: Connecting to GitHub

  1. Install the {usethis} package:

    install.packages("usethis")

  1. Introduce yourself to git:

    usethis::use_git_config(user.name = "Louisa Smith", user.email = "louisahsmith@gmail.com")

When you make changes to your code, they will be associated with this name and email address (this doesn’t really matter for our purposes)

  • You only need to do this once

Installing packages

If you just updated R to a new “major” version, you will need to reinstall packages

  • I tend to do this as I need them rather than try to reinstall them all at once

    • RStudio tries to help!

Possible errors

Spelling the package or function’s name wrong, or not installing or loading the package

Using packages

If you are writing a script you will save, and will use several functions from this package

library(usethis)
use_git_config(user.name = "Louisa Smith", user.email = "louisahsmith@gmail.com"

If you are just running some quick code in the console or only need to use the package a few times in a script

usethis::use_git_config(user.name = "Louisa Smith", user.email = "louisahsmith@gmail.com")

I try to only run library(package) from a script (not the console) so that there’s a “record” of me loading the package, or else I might accidentally write code that doesn’t work later

Since I don’t need to run this once, I would probably run this from the console (bottom) rather than a script (top)

Running from the console is great for install.packages(), quick calculations, fiddling with code until you get it right, or scenarios like this – otherwise save your code in a script!

Connect to GitHub

  1. Create a github token:

    usethis::create_github_token()

Instead of entering your password every time, this is a secure way to connect to GitHub

  • If you are ever asked for your GitHub password in RStudio, you have to give this instead

Connect to GitHub

  1. Copy the token

  2. Back in R, run this code and paste your token where it says “Enter password”:

    gitcreds::gitcreds_set()

You can do this again whenever your token expires or you are using a different device

Exercises

  • Refer back to the slides as needed
  • Ask a classmate if you’re stuck
  • Raise your hand for the teaching team
  • Done early? Help a friend! Read the resources section! Play around in R! Check your email!
15:00