Data Science with R for the Life Sciences

Basic Reproducibility

Notes

Make sure that Tools -> Global Options -> General -> Save workspace to ~/.RData on exit is set to the default Ask

Introduction to Reproducibility

  • Goal - rerun full analysis with a single click (or command)
  • First step - Make sure your code runs anytime and anywhere
    • next day (who has gotten code working & had it not work the next day?)
      • desktop vs. laptop
      • collaborators
      • advisor

Make sure things you did before don’t matter

  • Computers store the results of each command run in sequence
  • Change something
  • Looks like it still works
  • Only works because of something you did earlier in the same session
  • Start new project
  • Create data subdirectory
  • Use Right Click -> Save Link As to download Portal surveys & species data
data_mammals <- read.csv('data/surveys.csv')
avg_mass <- mean(data_mammals$weight, rm.na = TRUE)
  • You then go to add the species data and realize that data_mammals probably isn’t descriptive enough
data_surveys <- read.csv('data/surveys.csv')
avg_mass <- mean(data_mammals$weight, rm.na = TRUE)
data_species <- read.csv('data/species.csv')
  • And you rerun all of your code and everything works
  • But will it work after I restart R?
    • No, because the code doesn’t create data_mammals anymore
    • Read through code
  • Clear R environment using the broom icon on the Environment tab.
    • Doesn’t unload packages
    • Useful when developing code
  • Restart R to get a clean environment: Session -> Restart R
    • Does unload packages
    • Useful for making sure everything works
    • As long is it doesn’t secretly reload things
  • Run entire file using Source button or Ctrl-Shift-S

  • Makes sure that the code runs fully and produces desired result

  • Stop R from storing the state of the environment
  • When you close RStudio it will often ask if you want to save your workspace
  • Start to close RStudio
  • Show Save dialog
  • Or on RStudio Cloud it will just do this automatically
  • If you do this is will get reloaded when you start R, even when you restart it as described above
  • Stop this by Tools -> Global Options -> General -> Save workspace to ~/.RData on exit -> Never
  • Unclick Restore .RData into workspace at startup

Make sure code works on other computers

  • Don’t use setwd()
    • Use projects and relative paths
    • data/mydata.csv not C:\Users\Batman\DataCarp\data\mydata.csv
  • Write code that works on all operating systems * Filenames in code should match actual names exactly, including capitalization * Use / instead of \ or \\ in paths

Clean up extra code

  • Remove experiments from your code
  • Remove install.packages() lines from your code
  • Avoid reinstalling packages repeatedly

Checklist

  • There is an Assignment Turn In Checklist to help
  • Show link on main page