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INTRODUCTION TO R
Introducción a la Ciencia de Datos

Coral del Val Muñoz

Dept. Ciencias de la Computación e Inteligencia Artificial,

Universidad de Granada
Dept. Molecular Biophysics, German Cancer Research Center Heidelberg, Alemania
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Index
• Introduction to R • Data input and Output
• Rstudio • Examining Datasets
• Getting Started - R Console • Selecting subsets
• Help • Merging datasets
• R-workspace • Numerical Sumaries
• Packages • Useful functions
• Data types and Structures
• Vectors
• Missing and special values
• Matrices and Arrays
• Factors
• Lists
• Data frames
• Indexing
• Conditional indexing
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Lists
• Lists can be used to combine objects (of possibly different kinds/sizes) into a
larger composite object.
• The components of the list are named according to the arguments used.
• Components can be extracted with the double bracket operator [[ ]]
• Alternatively, named components can be accessed with the "$" separator.

> A<-c(31,32,40) Indexing Lists

> S<-as.factor(c("F","M","M","F"))
> People<-list(age=A,sex=S) > People[[1]]
> People [1] 31 32 40
$age
[1] 31 32 40 > People$age
$sex [1] 31 32 40
[1] F M M F
Levels: F M
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Names
Names of an R object can be accessed and/or modified with
the names() function.
z <- list(a = 1, b = "c", c = 1:3)
> z
$a
[1] 1
# change just the name of the third element.
$b names(z)[3] <- "c2”
[1] "c" z
$c
[1] 1 2 3 $a
[1] 1

$b
[1] "c"

$c2
[1] 1 2 3
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Input/Output: Keyboard and Monitor

•Suppose we have a file (file.txt) with this content:
12
2 5
641
scan("file.txt")
Read 4 items
[1] 12 2 5 641
scan("file.txt",what=character())
Read 4 items
[1] "12" "2" "5" “641"
scan(“file.txt",sep="\n")
Read 3 items
[1] 12 25 641
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Input/Output: Keyboard and Monitor

• Use scan() to read from the keyboard by specifying
an empty string for the filename:
scan("")
1: 23 4
3: 2
4:
Read 3 items
[1] 23 4 2

• Note that we are prompted with the index of the next

item to be input, and we signal the end of input with
an empty line.
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Input/Output: Keyboard and Monitor

• To read in a single line from the keyboard use
readline():
readline("Input data: ")
Input data: 23 4 2
[1] "23 4 2"

• Note that we are prompted with the index of the

next item to be input, and we signal the end of
input with an empty line.
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Input/Output: Print to the screen

•print() is a generic function, so the function
call depends on the class of the object that is
printed.
• If, for example, the argument is of class table,
then the print.table() function will be
called.
x <- 1:3

print(x^2)

[1] 1 4 9
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Input/Output: Print to the screen

• It is better to use cat() instead of print(), as
the latter can print only one expression and its
output is numbered:

x <- 1:3
print(x^2)
[1] 1 4 9
cat(x^2)
1 4 9
cat(x^2, x, "hola")
1 4 9 1 2 3 hola
cat(x^2, x, "hola", sep="_")
1_4_9_1_2_3_hola
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Input/Output: Reading and Writing files

• We will use of the function read.table() to
read in a data frame.
• Suppose we have a file matrix.txt with the
following content:

nombre edad
John 25
Mary 28
Jim 19
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Input/Output: Reading and Writing files

• The first line contains an optional header, specifying column
names. We could read the file this way:
read.table("matrix.txt",header=TRUE)
nombre edad
1 John 25
2 Mary 28
3 Jim 19

• Note that scan() would not work here, because our file
has a mixture of numeric and character data (and a
header).
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Input/Output: Reading and Writing files

• If we want to write a file, we change
read.table() for write.table() function:

write.table(matrix(1:6, nrow=2), "output.txt",

row.names=FALSE, col.names=FALSE)

output.txt:
1 3 5
2 4 6
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Input/Output: Reading and Writing files

• The function cat() can also be used to write
to a file, one part at a time:

cat("abc\n",file="u.txt")
cat("de\n",file="u.txt",append=TRUE)

u.txt:
abc
de
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Exporting Data: cat()

R objects can be exported to a text file using the cat() function:

cat (x , file = "", sep = " ", fill = FALSE, labels

= NULL, append = FALSE)

x: R object
file: character string naming the file to print to. If "" (the
default), cat prints to the console unless redirected by sink.
sep: a character vector of strings to append after each element
fill: controls how the output is broken into successive lines.
append: logical. If TRUE output will be appended to file;
otherwise, it will overwrite the contents of file.
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Read data from an excel: read.csv()

• Use R to read the file in .csv format:

# first row contains variable names, comma is

separator
# assign the variable id to row names
# note the “/” instead of “\” on mswindows systems

mydata <- read.csv("c:/mydata.csv", header=TRUE,

sep=",", row.names="id")
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read.delim()
• They are intended to read TAB separated files

read.delim(file, header = TRUE, sep = "\t", dec=".”,

fill =TRUE, ...)

• sep: the field separator character. “\t” (default for

read.delim) stands for TAB separator;

•fill: if TRUE then in case the rows have unequal length,

blank fields are implicitly added
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Read data from an excel: read.csv2()

• Use R to read the file in .csv format from countries that
use a comma (“,”) as decimal point and a semicolon
(“;”) as field separator.
# first row contains variable names, comma is
separator
# assign the variable id to row names
# note the “/” instead of “\” on mswindows systems

mydata <- read.csv2("c:/mydata.csv", header=TRUE,

sep=“;", dec=",“, row.names="id")
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Read data from SPSS: spss.get()

# Import international.sav as a data frame: demo

demo <- read.spss("international.sav",
to.data.frame = TRUE)

Read data from SPSS: read.dta()

# input Stata file
library(foreign)
mydata <- read.dta("c:/mydata.dta")
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Read data from JSON Files: fromJSON()

# Activate `rjson`
library(rjson)

# Import data from json file

JsonData <- fromJSON(file= "<fichero.json>" )

# Import data from json file through an URL

JsonData
<- fromJSON(file= "<URL al fichero JSON >" )
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Exporting Data
There are numerous methods for exporting R objects into
other formats . For SPSS, SAS and Stata you will need to
load the foreign packages. For Excel, you will need the
xlsReadWrite package.

• To an Excel Spreadsheet
library(xlsReadWrite)write.xls(mydata, "c:mydata.xls")
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Writing data frames

• write() writes out a matrix or vector in a specified number
of columns.

• write.table() writes out a data frame (or an object that can

be coerced to a data frame) with row and column labels

write.table(mydata, "c:/mydata.txt", sep="\t")

write.table(x, file = "", append = FALSE, sep = "

“, na = "NA", dec = ".", row.names = TRUE,
col.names = TRUE)
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Source Codes: Input

The input can come from a script file (a file containing R commands)

The source( ) function runs a script in the current session. If the filename
does not include a path, the file is taken from the current working
directory.
# input a script
source("myfile")
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Source Codes: Output

The sink( ) function defines the direction of the output.

# output directed to output.txt

# output overwrites existing file. no output to
terminal.
sink("myfile.txt", append=TRUE, split=TRUE)

# return output to the terminal

sink()
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Anexos
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Useful Packages for Data Analysis

Pre-modeling Post-modeling
Modeling stage
stage stage

Data visualization: Continuous regression:

ggplot2, googleVis car, randomforest General Model Validation:
LSMeans, Comparison
Data Transformation: Ordinal Regression:
plyr, dplyr, data.table Rminer, CoreLearn
Regression Validation:
Missing value Imputations: Classification: RegTest, ACD
Missforest, MissMDA Caret, BigRF

Outliers Detection: Clustering:

Outliers, EVIR CBA, RankCluster Clasification Validation:
ClustEval, SIgClust
Feature selection: Time Series:
Features, RRF, Boruta forecast, LTSA
ROC Analysis: PROC,
Dimension Reduction: Survival: TimeROC
FactoMineR, CCP survival, Basta
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General Subsetting Rules

Subsetting syntax:

# Subsetting of one dimensional objects (e.g.vectors,

factors)

my_object[row]

# Subsetting of two dimensional objects,(e.g. matrices,data

frames).

my_object[row, col]

# Subsetting of three dimensional objects, like arrays.

my_object[row, col, dim]
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General Subsetting Rules

There are three possibilities to subset data objects

(1) Subsetting by positive or negative index/position numbers

# Creates a vector sample with named elements.

my_object <- 1:26;
names(my_object) <- LETTERS

# Returns the elements 1-4.

my_object[1:4]

# Excludes elements 1-4.

my_object[-c(1:4)]
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General Subsetting Rules

There are three possibilities to subset data objects

(2) Subsetting by same length logical vectors

# Generates a logical vector as example.

my_logical <- my_object > 10

# Returns the elements where my_logical contains TRUE

values.
my_object[my_logical]

(3) Subsetting by field names

# Returns the elements with element titles: B, K, M

my_object[c("B", "K", "M")]
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Character Functions
Function Description
substr(x, start=n1, stop=n2) Extract or replace substrings in a character vector.
x <- "abcdef"
substr(x, 2, 4) is "bcd"
substr(x, 2, 4) <- "22222" is "a222ef"

grep(pattern, x , Search for pattern in x. If fixed =FALSE then pattern is a regular expression. If
ignore.case=FALSE, fixed=FALSE) fixed=TRUE then pattern is a text string. Returns matching indices.
grep("A", c("b","A","c"), fixed=TRUE) #returns 2

sub(pattern, replacement, x, Find pattern in x and replace with replacement text. If fixed=FALSE then pattern is
ignore.case =FALSE, fixed=FALSE) a regular expression.
If fixed = T then pattern is a text string.
sub("\\s",".","Hello There") returns "Hello.There"

strsplit(x, split) Split the elements of character vector x at split.

strsplit("abc", "") returns 3 element vector "a","b","c"

paste(..., sep="") Concatenate strings after using sep string to seperate them.
paste("x",1:3,sep="") returns c("x1","x2" "x3")
paste("x",1:3,sep="M") returns c("xM1","xM2" "xM3”)

toupper(x) Uppercase
tolower(x) Lowercase
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Gracias…