What is R and Rstudio

R is a powerful programming language for data analysis, statistics, visualisation and more. RStudio is the program that interacts between you and the language R. R and RStudio are two free available software with a huge community of users and developers.³

What are we going to learn?

At the end of this session you will be able to:

Create a project for data analysis
Create a folder/directory structure
Understand and move around layouts
Know where to find help
Import files/datasets
Know where packages are

Rstudio interaction

Please create a folder called “RProjects” under “Documents” This is important for our project data management.

Exercise 1 - New Rstudio Project (4 min)

⁴

RStudio menu (top left corner): click “File” menu button, then “New Project”
Click “New Directory”
Click “New Project” (“New empty project” if you have an older version of RStudio)
In Directory name type the name of your project, e.g. “RStudio_Intro” (Browse and select a folder where to locate your project, e.i. the RProjects folder)
Click the “Create Project” button

Panes or panels

There are four main panels on RStudio.

The upper-left panel is the editor where we interact with scripts.
The pane in the upper-right, where it says “Environment is empty,” will show the objects that you are currently working with.
The lower-left panel is called the console, which runs the R code. It is a testing ground and only saves the code temporarily.
The panel in the bottom-right will display results, files, help and more.

Exercise 2 - Folder structure (3 min)

Create three folders in your project⁵. Remember to use naming conventions or check⁶.

scripts
data
plots

Exercise 3 - New R script (2 min)

RStudio menu (top left corner): click “File” menu button, then “New File”, then “R script”. You can also create a new script with the shortcut “Ctrl+Shift+N” for mac users use “cmd” instead of “ctrl”.⁷
Save your script. You can click on the save icon or “Ctrl+S”. Select the scripts folder and type a name i.e. “learning.R”

Functions

How to get help

There are three ways to find help using RStudio⁸

?functioname
help(functioname)
Press F1 or “cmd F1” on the functioname

Exercise 4 - Check the description of these functions (2 min)

sessionInfo
list.files
ls

Exercise 5 - Add comments to your new R script file (3 min)

Comments start with #.

# Description:
# Author:
# Date:

To add a section

# Starting with objects --------------------------

R syntax

To get the hang of R, we start using it as a simple calculator. Type 2 + 2 directly into the console panel and press enter. You should see this:

2 + 2

## [1] 4

R variables or objects

R can calculate and store multiple values in variables or objects so we can access them later. Use: objectname <- value.

Notice the assignment operator <-
Value can be a given value or a result of a calculation or transformation

R Style

I recommend two style guides:

R data types

numeric
character
logical

Data structures

vector
factor
list
matrix
dataframe

Example of a numeric vector

many_numbers <- c(1, 2, 5.3, 6, -2, 4) # numeric vector
many_numbers

## [1]  1.0  2.0  5.3  6.0 -2.0  4.0

Exercise 6 - Create a vector (3 min)

You can create either a vector of characters or a vector of logicals

If you create a vector of characters use quotes "" for each value
If you create a vector of logicals use TRUE and FALSE

## [1] "one"   "two"   "three"

## [1]  TRUE  TRUE FALSE

Import files

Let’s introduce some data to R

download.file(url = "http://tiny.cc/csvexample", 
              destfile = "data/example.csv")

mydata <- read.csv(file = "data/example.csv")

Exercise 7 - Importing data into R (3 min)

You can either download the example csv file or copy another csv file to the data folder.
Read the csv file using read.csv ⁹
checkout the function str with your new object

Tip¹⁰

Install packages

Most R package you can be installed it like this: install.packages("packagename")

Then you need to load it using library(packagename)

Then go to the fourth panel and select the packages tab, after loading a package it should be checked.

You can also check sessionInfo()

Exercise 8 - Install the ggplot2 package for graphics (3 min)

Use what you have learned to install the ggplot2 package. If you are keen you can install the tidyverse package.

Close project

“File” “close project” (It asks if you want to save your data), then you can close RStudio.

Resources

There are plenty of R resources, this is only a short list.

Feedback

Please send your annonymous feedback through this link http://tiny.cc/elixir_feedback

Open source

This handout was written in Rmarkdown, and uses the open-source Tufte style. It has been published on Github pages and also as a PDF handout.

All of the information of my courses can be found on my Github repo R for Data Analysis. These resources are freely available under the Creative Commons - Attribution Licence. You may re-use and adapt the material in any way you wish, without asking permission, provided you cite the original source. That is a link back to the website R for Data Analysis and my ORCID 0000-0002-8990-1985.

I acknowledge this publication is resulting from support of Elixir-Belgium for my role as data science and bioinformatics trainer.

Last update: 2018-02-09

See installation instructions installation.md ↩
“Learning to code is a never ending journey with a set of challenges and delights unique to each person”↩
resources ↩
FYI: Projects make managing multiple directories straightforward↩
In RStudio, you can use the fourth panel then click “Files” then “New Folder”. Or you can use the function dir.create↩
a style guide ↩
You can run code from a script using “Ctrl+Enter” (line by line or a selection of code)↩
The help panel will show you the Documentation. How to use a function, input, details, and examples↩
You can also read other kinds of file using read.table or special packages↩
Always use the help in RStudio if you don’t know how a function works↩

RStudio Intro Handout

Paula Andrea Martinez

2018-01-23

Getting started

Hands-on Training

Starting with programing

Remember