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

Some R background

is a programming language and free software environment for statistical computing and graphics supported by the R Foundation for Statistical Computing.

Some R background

• 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

• 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

RStudio, the R IDE

• free
• open source

An interface

The same console as before

R as a calculator

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

R as a calculator

1 + 100
1 +

3 + 5 * 2

(3 + 5) * 2

(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

2/10000

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

5e3

Mathematical functions

log(1)  # natural logarithm

log10(10) # base-10 logarithm

exp(0.5)

Compute the factorial of 9

factorial(9)

Comparing things

equality (note two equal signs read as “is equal to”)

1 == 1

inequality (read as “is not equal to”)

1 != 2 

less than

1 < 2

less than or equal to

1 <= 1

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

Variables and assignment

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

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

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.

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

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

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

help(log)

?log

Various output

Functions are also variables

Test that your logarithm function can work in base 10

10^logarithm(12, base = 10)

Functions are also variables

We can also define our own function with

<FUNCTION_NAME> <- function(a, b){
  <RESULT_1> <- <OPERATION_1>(a, b)
  <RESULT_2> <- <OPERATION_2>(<RESULT_1>, b)
  return(<RESULT_2>)
}

write a function to test the base of the logarithm function