• R and RStudio are two separate but connected things
  • R is like the engine of your car
  • RStudio is the 'cabin' we use to interact with the engine
  • RStudio even comes with extra flashy features not related to R
• R does all the calculations, manages the data, generates plots
• RStudio helps manage our code, displays the plots plus more

• Some very helpful features of RStudio
  • We can write scripts and execute code interactively
  • Auto-completion by hitting the <tab> key
  • Use of R Projects to manage code/data for each project/analysis
  • We can see everything we need (directories, plots, code, history etc)
  • Integration with markdown, \(\LaTeX\), bash, python, C++, version control software etc.

1. Create a folder on your computer for today's material
   • We recommend Documents/R-Training-20170501 in your home folder
   • Create a sub-folder called data
2. Go to https://uofabioinformaticshub.github.io/Roseworthy-R-20170501/
   • Download the data file toothData.csv into
     Documents/R-Training-20170501/data
3. Now we can open RStudio

1. File > New Project > Existing Directory >
   • Browse to Documents/R-Training-20170501
   • Create Project

• R Projects are simply a wrapper for keeping an analysis organised
• The R Project name will always be the directory name
• Not essential, but are good practice and extremely useful

• The R Console is the engine
• We can enter code directly here
• We can even use this as a simple calculator

1 + 1

## [1] 2

2*2

## [1] 4

As well as performing simple calculations:

• R has what we call an Environment (i.e. a Workspace)
• We can define objects here, or import data
• Like a worksheet in Excel, but much more flexible & powerful
• R performs calculations & runs processes on these objects

To create an R object:

• We need to give it a name, and some data
• The process looks like nameOfObject <- data
  • The <- symbol is like an arrow
  • Tells R to put the data in the object

In the Console type:

x <- 2
y <- 3

• We have created two objects, x and y
  • Look in your Environment Tab
  • This Tab tells us what objects are currently in the Global Environment

• We can now call these objects by name
• To see the value of an object, type it's name

x

## [1] 2

y

## [1] 3

• We can also use them in calculations

x + y

## [1] 5

x / y

## [1] 0.6666667

NB: R is case sensitive

R has a series of inbuilt functions, e.g. sqrt(), log(), max(), min() etc

• We place an object or value inside the () after the name of a function

sqrt(x)

## [1] 1.414214

log(x)

## [1] 0.6931472

• These functions are organised into a package called base
  • Always installed with R
  • Groups similar functions together

?base

Click on the underlined word Index at the bottom for a list of these