Chapter 1 Prerequisites

1.1 Installing software

Please have these both installed (come early if you need help):

  • R: Download from here
    • MacOS users
      • Click on the “Download R for (Mac) OS X” link at the top of the page
      • Click on the .pkg file containing the latest version of R (currently 3.6.0) and save it to your computer. Double-click this file to run it and follow the installation instructions
    • Windows users
      • Click on the “Download R for Windows” link at the top of the page
      • Click on the “base” link
      • Click the “Download R 3.6.0 for Windows” and save the .exe file to your computer. Double click this file to run it and follow the installation instructions
  • RStudio: Download from here
    • MacOS users
      • Click on the latest Mac OS X version and save the .dmg file on your computer. Double-click the file to run it and follow the installation instructions
    • Windows users
      • Click on the latest Windows 7+ version and save the .exe file on your computer. Double-click the file to run it and follow the installation instructions

You may also use R and RStudio in a web browser. This method requires you to login with either a Gmail or GitHub account.

1.2 Downloading sample data

This book works from the following files of fake clinical data, that can be downloaded from the following links:

  1. messy_demographic.csv
  2. messy_cognitive.csv
  3. messy_genotype.csv

1.3 RStudio environment

Welcome to RStudio! You should see 4 window panes:

  1. Source
  • Your script! everything you do to your data should be typed here!! It saves what you are doing in a file ending in .R
  1. Console
  • The place where the good stuff happens. When you run a command, you see the output here.
  1. Enviroment/History
  • Environment: a list of everything in your “Workspace”
  • History: a list of every command you have run
  1. Files/Plots/Packages/Help
  • Files: a file browser (like Windows Explorer or Finder)
  • Plots: your plots will show up here
  • Packages: a list of all the packages you have installed with checkboxes indicating whether they are loaded
  • Help: your help documentation with be shown here

1.4 Loading libraries / installing packages

For this tutorial, we are going to use the packages tidyverse, tableone, rms and car. Please install them if you haven’t done so already.

install.packages(c("tidyverse", "rms", "tableone", "car"))
  • Look at the Packages Tab
  • Click on the check box to the left of “ggplot2”
  • Notice that a bunch of lines start running in Console window to show you that the package is loading
  • Go to the History Tab (top right corner)
  • Notice that you should library(ggplot2) has just run
  • Click on these lines to highlight them, then click on To Source at the top of the panel
  • This moves the lines we just ran into our script so we can re-run this step tomorrow!

1.5 Cheat Sheets

There are several cheat sheets available online that provide a quick reference when working with functions in the tidyverse.