Name: R Basics
Author: Lieven Clement

R Basics (2020–2021)

Lieven Clement · Universiteit Gent

In this interactive course you will build a foundation in R and learn the basics to wrangle data. The course is based on the first part of the e-book Introduction to Data Science authored by Prof. Rafael Irizarry, Department of Data Sciences at the Dana-Farber Cancer Institute and Department of Biostatistics Harvard School of Public Health.

You are not a member of this course.

Exercise series

Prologue

		Title	Class progress
		Preface
		Acknowledgments
		Introduction

Installing R and Rstudio

The instructions below include screen shots from the installation process in which we used the Chrome browser which, although not necessary, you can freely download and install from here: https://www.google.com/chrome/.

		Title	Class progress
		36.1 Installing R
		36.2 Installing RStudio

1. Getting started with R and RStudio

		Title	Class progress	Status
		1.1. Why R?
		1.2. The R console
		1.3. Scripts
		1.4. RStudio
		1.5. Installing R packages

2. R Basics

In this book, we will be using the R software environment for all our analysis. You will learn R and data analysis techniques simultaneously. To follow along you will therefore need access to R. We also recommend the use of an integrated development environment (IDE), such as RStudio, to save your work. Note that it is common for a course or workshop to offer access to an R environment and an IDE through your web browser, as done by RStudio cloud. If you have access to such a resource, you don’t need to install R and RStudio. However, if you intend on becoming an advanced data analyst, we highly recommend installing these tools on your computer. Both R and RStudio are free and available online. We suggest to develop your code for the exercises in RStudio and to paste your script in dodona to evaluate them.

		Title	Class progress	Status
		2.1 Case study: US Gun Murders
		2.2 The very basics
		2.3.1. Sum of integers 1,...,100
		2.3.2. Sum of integers 1,...,1000
		2.3.3. Interpret code
		2.3.4. Nested functions
		2.3.5. Interpret code
		2.4 Data types
		2.5.1. Variables in a dataframe
		2.5.2 Variable names
		2.5.3 Examining Variables
		2.5.4 Multiple ways to access variables
		2.5.5 Factors
		2.5.6 Tables
		2.6 Vectors
		2.7 Coercion
		2.8.1-5. Vectors
		2.8.6. Vector of numbers 12..73
		2.8.7. Odd numbers
		2.8.8. Length of a sequence
		2.8.9. Class of seq(1, 10, 0.5)
		2.8.10. Class of seq(1, 10)
		2.8.11. 1 vs 1L
		2.8.12. Vector cast
		2.9 Sorting
		2.10.1-4. Dataframes 1
		2.10.5-6. Dataframes 2
		2.10.7-8. NA
		2.11 Vector arithmetics
		2.12.1. Convert Temperatures
		2.12.2. Vector Sum
		2.12.3. Vector Mean
		2.13 Indexing
		2.14.1-5. Dataframe operations
		2.14.6. Match function
		2.14.7-8. Match operator
		2.15 Basic plots
		2.16.1. Scatter Plot
		2.16.2. Histogram
		2.16.3. Boxplot

3. Programming basics

We teach R because it greatly facilitates data analysis, the main topic of this book. By coding in R, we can efficiently perform exploratory data analysis, build data analysis pipelines, and prepare data visualization to communicate results. However, R is not just a data analysis environment but a programming language. Advanced R programmers can develop complex packages and even improve R itself, but we do not cover advanced programming in this book. Nonetheless, in this section, we introduce three key programming concepts: conditional expressions, for-loops, and functions. These are not just key building blocks for advanced programming, but are sometimes useful during data analysis. We also note that there are several functions that are widely used to program in R but that we will not cover in this book. These include split, cut, do.call, and Reduce, as well as the data.table package. These are worth learning if you plan to become an expert R programmer.

		Title	Class progress	Status
		3.0 Introduction
		3.1 Conditional expressions
		3.2 Defining functions
		3.3 Namespaces
		3.4 For-loops
		3.5 Vectorization and functionals
		3.6.1 Conditional expression
		3.6.2 Any and all
		3.6.3 Conditional changes
		3.6.4 Sum of the first n integers
		3.6.5 Functions with multiple variables
		3.6.6 Namespace
		3.6.7-8 Sum of the first n squares (I)
		3.6.9 Sum of the first n squares (II)
		3.6.10 Sum of the first n squares (III)

4. The tidyverse

Up to now we have been manipulating vectors by reordering and subsetting them through indexing. However, once we start more advanced analyses, the preferred unit for data storage is not the vector but the data frame. In this chapter we learn to work directly with data frames, which greatly facilitate the organization of information. We will be using data frames for the majority of this book. We will focus on a specific data format referred to as tidy and on specific collection of packages that are particularly helpful for working with tidy data referred to as the tidyverse.

We can load all the tidyverse packages at once by installing and loading the tidyverse package:

library(tidyverse)

We will learn how to implement the tidyverse approach throughout the book, but before delving into the details, in this chapter we introduce some of the most widely used tidyverse functionality, starting with the dplyr package for manipulating data frames and the purrr package for working with functions. Note that the tidyverse also includes a graphing package, ggplot2, which will be introduced in a later course on data visualization, the readr package discussed in Chapter 5; and many others. In this chapter, we first introduce the concept of tidy data and then demonstrate how we use the tidyverse to work with data frames in this format.

		Title	Class progress	Status
		4.1 Tidy data
		4.2.1 CO2
		4.2.2 Weight
		4.2.3 BOD
		4.2.4 Some more datasets
		4.3 Manipulating data frames
		4.4.1-3. Dataframe column operations
		4.4.4-6. Dataframe row operations
		4.4.7. Dataframe mixed operations
		4.5 The pipe: %>%
		4.6.1 Pipes
		4.7 Summarizing data
		4.8 Sorting data frames
		4.9.1. Summarizing
		4.9.2. Grouping
		4.9.3. Sorting
		4.10 Tibbles
		4.11 The dot operator
		4.12 do
		4.13 The purrr package
		4.14 Tidyverse conditionals
		4.15.1. Tibbles 1
		4.15.2. Tibbles 2
		4.15.3. Purrr

5. Importing Data

		Title	Class progress	Status
		5.0 Introduction
		5.1 Paths and the working directory
		5.2 The readr and readxl packages
		5.3 Lost column headers
		5.4 Downloading files
		5.5 R-base importing functions
		5.6 Text versus binary files
		5.7 Unicode versus ASCII
		5.8 Organizing data with spreadsheets
		5.9.1 Spreadsheets 1
		5.9.2 Spreadsheets 2