Intro to R for Bio and Enviro Sciences

Introduction to R

Notes

Have students open RStudio and check to see if console “sees” R.

R

  • Programming language
  • Started as a statistics and data analysis environment
  • But can also build websites, run simulations, and lots of other things
  • R is what runs all of the code we will write this semester
  • Separate from RStudio

RStudio

  • IDE - Integrated Development Environment
  • Makes developing code in R easier by including a number of tools in one place
  • Interpreter/Console is where R is actually running
    • Can work in here “interactively”
    • Run a single command and see the result
    • 2 + 2
    • This is also where RStudio will run code written in the text editor
  • Text editor
    • Where we write code we want to keep and potentially reuse later
    • Creates a plain text file that stores the code we’ve written
    • We can open it by clicking the New File button or using the Ctrl-Shift-N keyboard shortcut (Cmd-Shift-N) on Mac

Basic expressions

  • Write code directly in the text editor
  • Kangaroo rat weight (g -> lb)
50 / 1000 * 2.2
  • This is called an expression

  • A set of commands that returns a value

  • Run line
  • Run selection

  • Source & Source with Echo

  • Save as krat_weight_analysis.R in your Scripts folder
  • Can see in the Files tab that we’ve created this file
  • We can also use this tab to create, delete, and rename files & folders

Variables

  • To save the values we calculate for later use we use variables
  • A variable is a name that has a value associated with it
    • Assign using <- or =
    • you can insert <- using Alt + - (Windows) or Option + - (Mac)
weight_g <- 50
weight_g = 50
weight_g

  • We can see that this variable has been created by looking in the Environment tab

  • It works just like the value itself

weight_g / 1000
weight_g / 1000 * 2.2
weight_lb <- weight_g / 1000 * 2.2
  • It won’t change unless you assign a new value to it directly
weight_g
weight_g * 2
weight_g
weight_g <- 26
weight_g

RStudio tips

  • tab key autocompletes
    • Type wei and then tab
    • Let the computer do repetitious work.
    • It’s easier and with fewer mistakes.
  • And a history of the commands you’ve run under History in case you forgot to write something down

Comments

  • Remember what code is doing
  • For humans, not computers
  • Use the #
# Calculate weight of Kangaroo Rat in pounds

Assignments format

  • Comment before each problem and each sub-problem
  • Make sure result prints out on Source with echo
# Problem 1

# 1.1
2 + 2

# 1.2
2 - 8

# Problem 2

width = 2
height = 3
length = 1.5
volume = width * height * length
volume
  • save assignment scripts as “lastname_HW-number”
    • i.e., “Pomeranz_HW2”

Create assignment script, put in new folder

  • Now we’re going to work on some exercises to get a feel for this
  • In class we will often only do part of an exercise and save the rest for later

Do Exercise 1 - Basic Expressions

Do Exercise 2 - Basic Variables

Do Exercise 3 - More Variables at home

Functions

  • A function is a complicated expression.
  • Command that returns a value
sqrt(49)
  • A function call is composed of two parts.
    • Name of the function
    • Arguments that the function requires to calculate the value it returns.
    • sqrt() is the name of the function, and 49 is the argument.
  • We can also pass variables as the argument
weight_lb <- 0.11
sqrt(weight_lb)
  • Another function that we’ll use a lot is str() and class()
  • All values and therefore all variables have types
  • str, short for “structure”, lets us look at them
str(weight_lb)
class(weight_lb)
  • Another data type is for text data
  • We right text inside of quotation makes
"hello world"
  • If we look at the structure of some text we see that it is type character
str("hello world")
class("hello world")
  • Functions can take multiple arguments.
    • Round weight_lb to one decimal place
    • Typing round() shows there are two arguments
      • x Number to be rounded
      • digits number of digits
round(weight_lb, digits = 1)
  • Functions also work without naming arguments
round(weight_lb, 1)
  • Must put arguments in correct order

  • When learning, it’s best to name all arguments

  • Functions return values, so as with other values and expressions, if we don’t save the output of a function then there is no way to access it later
  • It is common to forget this when dealing with functions and expect the function to have changed the value of the variable
  • But looking at weight_lb we see that it hasn’t been rounded
weight_lb
  • To save the output of a function we assign it to a variable.
weight_rounded <- round(weight_lb, 1)
weight_rounded

Do Exercise 4 - Built-in Functions