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 anywhere
• Important for class - your code has to run the on graders computer
• Important for science
  • 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 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 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
• 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
• 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
  • Assume case specificity
    • Filenames in code should match actual names exactly, including capitalization
  • Use / instead of \ or \\ in paths

Use print to show things you want the program to show

• Depending on how your code is run it may show different things
• Source without echo will hide most things
• Use the print function to print out text you want the person running your code to see
• Print out the answers to each homework exercise

Clean up extra code

• Remove experiments from your code
• Remove install.packages() lines from your code
  • Avoid reinstalling packages on other peoples computers
  • If you really want to keep it comment it out

Checklist

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