Introduction to R Carolina Ferrari

Transcription

1 Introduction to R Carolina Ferrari carolina.ferrari01@universitadipavia.it Microbiology and Virology Unit, IRCCS Policlinico San Matteo

2 What is R? R is a system for statistical analyses (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering,...) and graphics. R is both a software and a language (S language). Good things about R - It's free - It works on all platforms (Linux, Windows, Mac) - It can deal with much larger datasets than Excel for example - Graphs can be produced to your own specification - It can be used to perform powerful statistical analysis - It is well supported and documented Bad things about R - It can struggle to cope with extremely large datasets - The environment can be daunting if you don't have any programming experience

3 How to install R Download R from the web page and install it. Select your version and click to download

4 How to install RStudio In this course we will use RStudio that is a GUI (Graphical User Interface) available for R. It is a graphical interface that helps the programmer making R more user-friendly. Download RStudio from the web page.

5 Select your version and click to download

6 Welcome to RStudio

7 R as calculator For sum, subtraction, multiplication and division operations use the usual symbols: + - * / Power elevation is used: ** or ^ > 18*2 [1] 36 > 2+3*4 [1] 14 > (2+3)*4 You should pay attention to the use of brackets [1] 20

8 Variable: in the context of programming, is a symbolic name given to an object (number, string, matrix,...) We can represent it as a box in which you put your object. In your program you will refer to your object using the name of the box (the name of the variable). e.g. if Kiwi is our object, we can put it into a variable called Fruits Fruits Kiwi

9 e.g. if Kiwi is our object, we can put it into a variable called Fruits Fruits Kiwi How to do it in R Assignment simbol variable_name <- "object_name" > Fruits <- "Kiwi" In R double quotes represent a string!! If you want to see what a variable contains, print the variable_name > Fruits [1] "Kiwi"

10 Vector: single entity consisting of an ordered collection of variables We can represent it as a box partitioned in many numbered sectors: in each sector you can put an object and then retrieve it knowing the vector name and the object's position in the vector. e.g. if Fruits is our vector we can fill it so Fruits Kiwi Apple Peach Pear

11 Fruits Kiwi Apple Peach Pear How to do it in R Function to combine values in a vector vector_name <- c("object_1", "object_2", "object_3", "object_4",...) > Fruits <- c("kiwi", "Apple", "Peach", "Pear") > Fruits [1] "Kiwi" "Apple" "Peach" "Pear" If a command is not complete at the end of a line, R gives a prompt, by default + on second and subsequent lines and continue to read input until the command is syntactically complete.

12 Function: is a procedure that gets one (or more) input (e.g a variable, a vector, a matrix, a number,...) and a list of parameters and do something with them How to do it in R arguments function_name(input, parameter1, parameter2,...) open and closed brackets If you want to save the result of the function into a variable: output_name <- function_name(input, parameter1, parameter2,...)

13 Fruits Kiwi Apple Peach Pear How to get an object from a vector: vector_name[position in the vector] > Fruits[2] [1] "Apple" How to know the length of a vector: length(vector_name) > length(fruits) [1] 4

14 Practice - Generate a vector of the seasons and call it Seasons - Determine the length of the vector - Extract the season of your birthday

15 Solution - Generate a vector of the seasons and call it Seasons - Determine the length of the vector - Extract the season of your birthday > Seasons <- c("winter", "Spring", "Summer", "Autumn") > Seasons [1] "Winter" "Spring" "Summer" "Autumn" > length(seasons) [1] 4 > Seasons[3] [1] "Summer" My birthday is August 10th, thus

16 Variable: in the context of programming, is a symbolic name given to an object Vector: single entity consisting of an ordered collection of variables Three ways to create a number vector: 1) colon operator : > t <- 1:16 > t [1] ) c( ) function > n <- c(13, 15, 11, 12, 19, 11, 17, 19, 46, 82, 24) > n [1] ) seq( ) function > p <- seq(1, 40, by=5) > p [1]

17 > n <- c(13, 15, 11, 12, 19, 11, 17, 19, 46, 82, 24) > n [1] How to reverse a vector: rev(vector_name) > rev(n) [1] How to sort a vector: sort(vector_name) > sort(n) [1]

18 > n <- c(13, 15, 11, 12, 19, 11, 17, 19, 46, 82, 24) > n [1] How to know the largest element of a vector: max(vector_name) > max(n) [1] 82 How to know the smallest element of a vector: mim(vector_name) > min(n) [1] 11 How to know minimum and maximum of all the given arguments: range(vector_name) > range(n) [1] 11 82

19 Matrix: is a two dimension collection of variables. 1 Kiwi Apple Peach Pear Rows 2 Winter Spring Summer Autumn 3 Brown Red Yellow Green Columns To build a matrix we have to use a specific R function

20 To build the matrix we use the function matrix 1 Kiwi Apple Peach Pear Rows 2 Winter Spring Summer Autumn 3 Brown Red Yellow Green Columns matrix_name <- matrix(vector of objects of the table, ncol=number of columns, nrow=number of rows, byrow=true) > Fruits <- matrix(c("kiwi", "Apple", "Peach", "Pear", "Winter", "Spring", "Summer", "Autumn", "Brown", "Red", "Yellow", "Green"), ncol=4, nrow=3, byrow=true)

21 byrow is a logical argument. If FALSE (the default) the matrix is filled by columns, otherwise the matrix is filled by rows byrow = TRUE byrow = FALSE

22 byrow is a logical argument. If FALSE (the default) the matrix is filled by columns, otherwise the matrix is filled by rows. Try to execute the command without byrow = TRUE

23 byrow is a logical argument. If FALSE (the default) the matrix is filled by columns, otherwise the matrix is filled by rows. > Fruits <- matrix(c("kiwi", "Apple", "Peach", "Pear", "Winter", "Spring", "Summer", "Autumn", "Brown", "Red", "Yellow", "Green"), ncol=4, nrow=3, byrow=true) > Fruits with byrow=true [,1] [,2] [,3] [,4] [1,] "Kiwi" "Apple" "Peach" "Pear" [2,] "Winter" "Spring" "Summer" "Autumn" [3,] "Brown" "Red" "Yellow" "Green" > Fruits <- matrix(c("kiwi", "Apple", "Peach", "Pear", "Winter", "Spring", "Summer", "Autumn", "Brown", "Red", "Yellow", "Green"), ncol=4, nrow=3) > Fruits without byrow=true [,1] [,2] [,3] [,4] [1,] "Kiwi" "Pear" "Summer" "Red" [2,] "Apple" "Winter" "Autumn" "Yellow" [3,] "Peach" "Spring" "Brown" "Green"

24 Practice Generate a matrix called Animals, with 3 columns and 2 rows, to represent the following: Animals Lion Cow Cat Carnivorous Erbivore Carnivorous

25 Solution 1 Generate a matrix called Animals, with 3 columns and 2 rows, to represent the following: Animals Lion Cow Cat Carnivorous Erbivore Carnivorous > Animals <- matrix(c("lion", "Cow", "Cat", "Carnivorous", "Erbivore", "Carnivorous"), ncol=3, nrow=2, byrow=true) > Animals [,1] [,2] [,3] [1,] "Lion" "Cow" "Cat" [2,] "Carnivorous" "Erbivore" "Carnivorous"

26 Solution 2 Generate a matrix called Animals, with 3 columns and 2 rows, to represent the following: Animals Lion Cow Cat Carnivorous Erbivore Carnivorous > animal_name <- c("lion", "Cow", "Cat") > diet <- c("carnivorous", "Erbivore", "Carnivorous") > Animals <- matrix(c(animal_name, diet), nrow=2, byrow=true) > Animals [,1] [,2] [,3] [1,] "Lion" "Cow" "Cat" [2,] "Carnivorous" "Erbivore" "Carnivorous" I used the c() function to concatenate two vectors!!

27 We can use the R help function to understand how to use a function: which kind of inputs it accepts and which parameters we can set >?function_name > help(function_name)

28 Practise at home Practice - Generate a vector called Exams with the subjects: Genetics, Microbiology, Bioinformatics, Mathematics, English - Generate a vector of five random numbers between 18 and 30. Call it Grades - Generate a matrix called University having 2 columns: Exams and Grades

29 Practise at home SOLUTION > Exams <- c("genetics", "Microbiology", "Bioinformatics", "Mathematics", "English") > Exams [1] "Genetics" "Microbiology" "Bioinformatics" "Mathematics" [5] "English" > Grades <- c(21, 26, 30, 18, 23) > Grades [1] > University <- matrix(c(exams, Grades), ncol=2) > University [,1] [,2] [1,] "Genetics" "21" [2,] "Microbiology" "26" [3,] "Bioinformatics" "30" [4,] "Mathematics" "18" [5,] "English" "23"