slides.Rmd

title: 'R#1: Introduction to R and RStudio'
author: "Laurent Modolo [laurent.modolo@ens-lyon.fr](mailto:laurent.modolo@ens-lyon.fr)"
date: "10 Oct 2019"
output:
  beamer_presentation:
    df_print: tibble
    fig_caption: no
    highlight: tango
    latex_engine: xelatex
    slide_level: 3
    theme: metropolis
  ioslides_presentation:
    highlight: tango
  slidy_presentation:
    highlight: tango

R#1: Introduction to R and RStudio

The goal of this practical is to familiarize yourself with R and the RStudio environment.

The objectives of this session will be to:

• Understand the purpose of each pane in RStudio
• Do basic computation with R
• Define variables and assign data to variables
• Manage a workspace in R
• Call functions
• Manage packages

Acknowledgments

\begin{columns} \begin{column}{0.5\textwidth} \includegraphics[width=\textwidth]{img/software_carpentry_logo} {\bf https://software-carpentry.org/} http://swcarpentry.github.io/r-novice-gapminder/ \end{column} \begin{column}{0.5\textwidth} \includegraphics[width=\textwidth]{img/r_for_data_science.png} \end{column} \end{columns}

Some R background

\includegraphics[width=40pt]{img/Rlogo.png} is a programming language and free software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing.

Some R background

\includegraphics[width=40pt]{img/Rlogo.png}

• Created by Ross Ihaka and Robert Gentleman
• initial version released in 1995
• free and open-source implementation the S programming language
• currently developed by the R Development Core Team.

Some R background

Reasons to use \includegraphics[width=40pt]{img/Rlogo.png}

• It’s free, well documented, and runs almost everywhere

• it has a large (and growing) user base among scientists

• it has a large library of external packages available for performing diverse tasks.

• 15,068 available packages on https://cran.r-project.org/

• 3,087 available packages on http://www.bioconductor.org

• 122,720 available repository on https://github.com/

Some R background

\includegraphics[width=\textwidth]{img/R_terminal.png}

RStudio, the R IDE

\begin{block}{IDR: Integrated development environment} application that provides {\bf comprehensive facilities} to computer programmers for software development \end{block}

• free
• open source

An interface

\includegraphics[width=\textwidth]{img/RStudio.png}

The same console as before

\includegraphics[width=\textwidth]{img/RStudio_console.png}

R as a calculator

• Add: +
• Divide: /
• Multiply: *
• Subtract: -
• Exponents: ^ or **
• Parentheses: (, )

R as a calculator

1 + 100
1 +

\pause

3 + 5 * 2

(3 + 5) * 2

\pause

(3 + (5 * (2 ^ 2))) # hard to read
3 + 5 * 2 ^ 2       # clear, if you remember the rules
3 + 5 * (2 ^ 2)     # if you forget some rules, this might help

\pause

2/10000

\pause

2e-4 is shorthand for 2 * 10^(-4)

5e3

Mathematical functions

log(1)  # natural logarithm

\pause

log10(10) # base-10 logarithm

\pause

exp(0.5)

\pause

Compute the factorial of 9

\pause

factorial(9)

Comparing things

equality (note two equal signs read as "is equal to")

1 == 1

\pause

inequality (read as "is not equal to")

1 != 2 

\pause

less than

1 < 2

\pause

less than or equal to

1 <= 1

\pause

greater than

1 > 0

Variables and assignment

<- is the assignment operator in R. (read as left member take right member value)

x <- 1/40

x

The environment

\includegraphics[width=\textwidth]{img/RStudio_environment.png}

Variables and assignment

log(x)
x <- 100
log(x)

\pause

x <- x + 1
y <- x * 2

\pause

z <- "x"
x + z

Variables and assignment

Variable names can contain letters, numbers, underscores and periods.

They cannot start with a number nor contain spaces at all.

Different people use different conventions for long variable names, these include

periods.between.words
underscores_between_words
camelCaseToSeparateWords

What you use is up to you, but be consistent.

\pause It is also possible to use the = operator for assignment but don’t do it !

Variables and assignment

Which of the following are valid R variable names?

min_height
max.height
_age
.mass
MaxLength
min-length
2widths
celsius2kelvin

http://perso.ens-lyon.fr/laurent.modolo/R/1_a

Functions are also variables

logarithm <- log

\pause

A R function can have different arguments

function (x, base = exp(1))

• base is a named argument are read from left to right
• named arguments breaks the reading order
• named arguments make your code more readable

\pause

To know more about the log function we can read its manual.

help(log)

\pause

?log

Various output

\includegraphics[width=\textwidth]{img/RStudio_outputs.png}

Functions are also variables

Test that your logarithm function can work in base 10

\pause

10^logarithm(12, base = 10)

Functions are also variables

We can also define our own function with

function_name <- function(a, b){
  result_1 <- operation1(a, b)
  result_2 <- operation2(result_1, b)
  return(result_2)
}

\pause

write a function to test the base of the logarithm function

\pause

base_test <- function(x, base){
  log_result <- logarithm(x, base=base)
  exp_result <- base^log_result
  test_result <- x == exp_result
  return(test_result)
}

http://perso.ens-lyon.fr/laurent.modolo/R/1_b

Functions are also variables

base_test <- function(x, base){
  print(x)
  log_result <- logarithm(x, base=base)
  print(log_result)
  exp_result <- base^log_result
  print(exp_result)
  print(x)
  test_result <- x == exp_result
  return(test_result)
}

http://perso.ens-lyon.fr/laurent.modolo/R/1_c

Functions are also variables

base_test <- function(x, base){
  print(x)
  log_result <- logarithm(x, base=base)
  print(log_result)
  exp_result <- base^log_result
  print(exp_result)
  print(x)
  test_result <- isTRUE(all.equal(x, exp_result))
  return(test_result)
}

http://perso.ens-lyon.fr/laurent.modolo/R/1_d

Functions are also variables

base_test <- function(x, base){
  return(isTRUE(all.equal(x, base^logarithm(x, base=base))))
}

http://perso.ens-lyon.fr/laurent.modolo/R/1_e

The environment

\includegraphics[width=\textwidth]{img/RStudio_environment.png}

A code editor

\includegraphics[width=\textwidth]{img/RStudio_editor.png}

A code editor

RStudio offers you great flexibility in running code from within the editor window. There are buttons, menu choices, and keyboard shortcuts. To run the current line, you can

• click on the Run button above the editor panel, or
• select “Run Lines” from the “Code” menu, or
• hit Ctrl+Return in Windows or Linux or Cmd+Return on OS X. To run a block of code, select it and then Run.

If you have modified a line of code within a block of code you have just run, there is no need to reselect the section and Run, you can use the next button along, Rerun the previous region. This will run the previous code block including the modifications you have made.

A code editor

Copy your logarithm and base_test into a tp_1.R file

\pause

We can now clean your environment

rm(x)

\pause

?rm

\pause

ls()

\pause

rm(list = ls())

Installing packages

install.packages("tidyverse")

install.packages("ggplot2")

Installing packages

\includegraphics[width=\textwidth]{img/RStudio_outputs.png}

Loading packages

sessionInfo()

\pause

library(tidyverse)

\pause

sessionInfo()

\pause

unloadNamespace("tidyverse")

\pause

sessionInfo()

Complex variable type

Vector (aka list)

c(1, 2, 3, 4, 5)

\pause

1:5

\pause

2^(1:5)

\pause

x <- 1:5
2^x

\pause

log(x)
logarithm(x)
base_test(x, base = 10)

Vector (aka list)

typeof(x)

\pause

typeof(x + 0.5)

\pause

is.vector(x)

\pause

y <- c(a = 1, b = 2, c = 3, d = 4, e = 5)
typeof(y)
is.vector(y)

\pause

x == y

\pause

all.equal(x, y)