Before we start

Learning Objectives

• Articulating motivations for this lesson
• Introduce participants to the RStudio interface
• Set up participants to have a working directory with a data/ folder inside

Basics of R

R is a versatile, open source programming/scripting language that’s useful for statistics and data science. It is inspired by the programming language S.

• Open source software under GPL. FREE
• Superior (if not just comparable) to commercial alternatives. R has over 7,000 user contributed packages at this time. It’s widely used both in academia and industry.
• Available on all platforms.
• Not just for statistics, but also general purpose programming.
• Is object oriented and functional.
• Reproducible Research- Data Management, Analysis/Code, and Manuscript Preparation
• Large and growing community of peers.

Let’s start by learning about our tool.

Point out the different windows in R.

• Lower Left: Console
  • this is where everything is executed
  • you can type into here and press enter to execute
• Upper Left: Scripts
  • this is where you compose the ordered execution of code that works well
  • highlight a chunk, and press “run” or Ctrl+R or Ctrl+Enter to execute
    • if your cursor is anywhere on the line it will run the whole line and advance the cursor to the next line
  • this is what you write and save to be executed at any time in the future
• Upper Right:
  • Environment
    • a list of all the variables, datasets, model outputs (“objects”) that you’ve created this session only
    • provides ways to explore the values of these things
  • History
    • a list of all commands executed in the console (without the output)
• Lower Right: (Everything else)
  • Files
    • a view of the project folder- what is available to you?
    • also called the “working directory” - it’s where you are working now
  • Plots
    • this is where your plots will show up when you make them
  • Packages
    • a list of all the “add on” packages that you can use and which you have loaded for use in this session
  • Help
    • where the help will show up.
      
    • search from the textbox
    • get help for a function (e.g. mean) by typing ?mean in the console
  • Viewer
    • This is advanced, don’t worry about this now

Setup

• Start RStudio (presentation of RStudio -below- should happen here)
• Under the File menu, click on New project, choose New directory, then Empty project
• Enter a name for this new folder, and choose a convenient location for it. This will be your working directory for the rest of the day (e.g., ~/data-carpentry)
• Click on “Create Project”
• Under the Files tab on the right of the screen, click on New Folder and create a folder named data within your newly created working directory. (e.g., ~/data-carpentry/data)
• Create a new R script (File > New File > R script) and save it in your working directory (e.g. data-carpentry-script.R)

Your working directory should now look like this:

Note that this is just a convenient way of viewing what is in this folder. Go to your windows browser to see how these mirror each other.

Next: Intro to R