Skip to content

Latest commit

 

History

History
99 lines (79 loc) · 3.23 KB

basic-reproducibility-R.md

File metadata and controls

99 lines (79 loc) · 3.23 KB
Raw
layout element title language
page
notes
Basic Reproducibility
R

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