“R” Programming Language

Tutorial

ECE 313 – Section B

University of Illinois at Urbana - Champaign
 Outline
• Why R, and R Paradigm
• References, Tutorials and links
• R Overview
• R Interface
• R Workspace
• Help
• R Packages
• Input/Output
• Reusing Results
 Why R?

• It's free!
• It runs on a variety of platforms including Windows, Unix and
MacOS.
• It provides an unparalleled platform for programming new
statistical methods in an easy and straightforward manner.
• It contains advanced statistical routines not yet available in
other packages.
• It has state-of-the-art graphics capabilities.
 Installing R
• How to download R:
– http://www.r-project.org/
– Google: “R”
– Windows, Linux, Mac OS X, source
– On mindhive:
• user@ba1:~$> R [terminal only]
• user@ba1:~$> R –g Tk & [application window]
• Files for this tutorial:
– http://web.mit.edu/tkp/www/R/R_Tutorial_Data.txt
– http://web.mit.edu/tkp/www/R/R_Tutorial_Inputs.txt
 Tutorials
• Each of the following tutorials are in PDF format.
• P. Kuhnert & B. Venables, An Introduction to R: Software for
Statistical Modeling & Computing
• J.H. Maindonald, Using R for Data Analysis and Graphics
• B. Muenchen, R for SAS and SPSS Users
• W.J. Owen, The R Guide
• D. Rossiter, Introduction to the R Project for Statistical Computing
for Use at the ITC
• W.N. Venebles & D. M. Smith, An Introduction to R
 Where to find R help and resources on the web
• R wiki:

ISBN: 9780596801700
http://rwiki.sciviews.org/doku.php
• R graph gallery:
http://addictedtor.free.fr/graphiques/thumbs.php
• Kickstarting R:
http://cran.r-project.org/doc/contrib/Lemon-kickstart/
 More Links
• R time series tutorial
• R Concepts and Data Types presentation by Deepayan Sarkar
• Interpreting Output From lm()
• The R Wiki
• An Introduction to R
• Import / Export Manual
• R Reference Cards
 Introduction
• R is “GNU S” — A language and environment for data
manipula-tion, calculation and graphical display.
– R is similar to the award-winning S system, which was developed at Bell
Laboratories by John Chambers et al.
– a suite of operators for calculations on arrays, in particular matrices,
– a large, coherent, integrated collection of intermediate tools for interactive
data analysis,
– graphical facilities for data analysis and display either directly at the computer
or on hardcopy
– a well developed programming language which includes conditionals, loops,
user defined recursive functions and input and output facilities.
 Introduction
• The core of R is an interpreted computer language.
– It allows branching and looping as well as modular programming using functions.
– Most of the user-visible functions in R are written in R, calling upon a smaller set
of internal primitives.
– It is possible for the user to interface to procedures written in C, C++ or
FORTRAN languages for efficiency, and also to write additional primitives.
 What R does and does not
o data handling and storage: o is not a database, but
numeric, textual connects to DBMSs
o matrix algebra o has no graphical user
interfaces, but connects to
o hash tables and regular
Java, TclTk
expressions
o language interpreter can be
o high-level data analytic and
very slow, but allows to call
statistical functions
own C/C++ code
o classes (“OO”)
o no spreadsheet view of data,
o graphics but connects to
o programming language: Excel/MsOffice
loops, branching, o no professional /
subroutines commercial support
 Some Useful Functions
• length(object) # number of elements or components
• str(object) # structure of an object
• class(object) # class or type of an object
• names(object) # names
• c(object,object,...) # combine objects into a vector
• cbind(object, object, ...) # combine objects as columns
• rbind(object, object, ...) # combine objects as rows
• ls() # list current objects
• rm(object) # delete an object
• newobject <- edit(object) # edit copy and save a
• newobject
• fix(object) # edit in place
 R Warning !

R is a case sensitive language.

FOO, Foo, and foo are three different objects
 Getting Help
> help(t.test)
> help.search("standard deviation")
Workspace
 R Workspace
– Objects that you create during an R session
are hold in memory, the collection of
objects that you currently have is called the
workspace. This workspace is not saved on
disk unless you tell R to do so. This means
that your objects are lost when you close R
and not save the objects, or worse when R
or your system crashes on you during a
session.
 R Workspace
• When you close the RGui or the R console window,
the system will ask if you want to save the
workspace image.
• If you select to save the workspace image then all
the objects in your current R session are saved in a
file .RData.
• This is a binary file located in the working directory
of R, which is by default the installation directory
of R.
 R Workspace
• During your R session you can also explicitly save
the workspace image. Go to the `File‘ menu and
then select `Save Workspace...', or use the
save.image function.
• ## save to the current working directory
• save.image()
• ## just checking what the current working directory is
• getwd()
• ## save to a specific file and location
• save.image("C:\\Program Files\\R\\R-2.5.0\\bin\\.RData")
 R Workspace
• If you have saved a workspace image and you start
R the next time, it will restore the workspace. So
all your previously saved objects are available
again. You can also explicitly load a saved
workspace le, that could be the workspace image
of someone else. Go the `File' menu and select
`Load workspace...'.
 R Workspace

# save your command history

savehistory(file="myfile") # default is ".Rhistory"
# recall your command history
loadhistory(file="myfile") # default is ".Rhistory“
 R Workspace
• To list the objects that you have in your current R session use the
function ls or the function objects.
> ls()
[1] "x" "y"

• So to run the function ls we need to enter the name followed by an

opening ( and and aclosing ). Entering only ls will just print the object,
you will see the underlying R code of the the function ls. Most
functions in R accept certain arguments. For example, one of the
arguments of the function ls is pattern. To list all objects starting with
the letter x:
> x2 = 9
> y2 = 10
> ls(pattern="x")
[1] "x" "x2"
Data Input
 Importing From A Comma
Delimited Text File
• first row contains variable names, comma is separator
• assign the variable id to row names
• note the / instead of \ on mswindows systems

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

row.names="id")
 Importing and exporting data
• There are many ways to get data into R and out of R.

• Most programs (e.g. Excel), as well as humans, know how to deal with
rectangular tables in the form of tab-delimited text files.

• > x = read.delim(“filename.txt”)
• also: read.table, read.csv

• > write.table(x, file=“x.txt”, sep=“\t”)

 Reading Data from Files
> myData <- read.table("R_Tutorial_Data.txt",
+ header=TRUE, sep="\t")
> myData
Condition Group Pre1 Pre2 Pre3 Pre4 Learning
1 Low A 0.77 0.91 0.24 0.72 0.90
2 Low A 0.82 0.91 0.62 0.90 0.87
3 Low A 0.81 0.70 0.43 0.46 0.90
. . .
61 High B 0.44 0.41 0.84 0.82 0.29
62 High B 0.48 0.56 0.83 0.85 0.48
63 High B 0.61 0.82 0.88 0.95 0.28
 Importing data: caveats
 Type conversions: by default, the read functions try to guess and autoconvert
the data types of the different columns (e.g. number, factor, character).
 There are options as.is and colClasses to control this – read the online
help
 Special characters: the delimiter character (space, comma, tabulator) and the
end-of-line character cannot be part of a data field.
 To circumvent this, text may be “quoted”.
 However, if this option is used (the default), then the quote characters
themselves cannot be part of a data field. Except if they themselves are
within quotes…
 Understand the conventions your input files use and set the quote
options accordingly.
 Keyboard Input

• You can also use R's built in spreadsheet to enter the data
interactively, as in the following example.
• # enter data using editor
mydata <- data.frame(age=numeric(0), gender=character(0),
weight=numeric(0))
mydata <- edit(mydata)
# note that without the assignment in the line above,
# the edits are not saved!
 Keyboard Input
• Usually you will obtain a dataframe by importing it from SAS,
SPSS, Excel, Stata, a database, or an ASCII file. To create it
interactively, you can do something like the following.

• create a dataframe from scratch

age <- c(25, 30, 56)
gender <- c("male", "female", "male")
weight <- c(160, 110, 220)
mydata <- data.frame(age,gender,weight)
 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.
 Exporting Data
To A Tab Delimited Text File
write.table(mydata, "c:/mydata.txt", sep="\t")
To an Excel Spreadsheet
library(xlsReadWrite)
write.xls(mydata, "c:/mydata.xls")
To SAS
library(foreign)
write.foreign(mydata, "c:/mydata.txt",
"c:/mydata.sas", package="SAS")
 Viewing Data
There are a number of functions for listing the contents of an object or
dataset.
# list objects in the working environment
ls()
# list the variables in mydata
names(mydata)
# list the structure of mydata
str(mydata)
# list levels of factor v1 in mydata
levels(mydata$v1)
# dimensions of an object
dim(object)
 Viewing Data
There are a number of functions for listing the contents of an object or
dataset.
# class of an object (numeric, matrix, dataframe, etc)
class(object)
# print mydata
mydata
# print first 10 rows of mydata
head(mydata, n=10)
# print last 5 rows of mydata
tail(mydata, n=5)
 Examining datasets
> plot(myData)
 Changing the Look of Graphics (I)
• The most likely change: orientation and size of labels of x and y axes:
> plot(xvalues,yvalues, ylab = "Label for y axis", xlab =
"Label for x axis", las = 1, cex.lab = 1.5)

• ylab, xlab : changes the annotation of the axis labels;

• las : numeric in {0,1,2,3} change orientation of the axis labels;

• cex.lab : magnification to be used for x and y labels;

• To get full range of changes about graphical parameters:

>?par
Working with Data
 Selecting Subsets of Data
> myData$Learning
[1] 0.90 0.87 0.90 0.85 0.93 0.93 0.89 0.80 0.98
[10] 0.88 0.88 0.94 0.99 0.92 0.83 0.65 0.57 0.55
[19] 0.94 0.68 0.89 0.60 0.63 0.84 0.92 0.56 0.78
[28] 0.54 0.47 0.45 0.59 0.91 0.98 0.82 0.93 0.81
[37] 0.97 0.95 0.70 1.00 0.90 0.99 0.95 0.95 0.97
[46] 1.00 0.99 0.18 0.33 0.88 0.23 0.75 0.21 0.35
[55] 0.70 0.34 0.43 0.75 0.44 0.44 0.29 0.48 0.28
> myData$Learning[myData$Group=="A"]
[1] 0.90 0.87 0.90 0.85 0.93 0.93 0.89 0.80 0.98
[10] 0.88 0.88 0.94 0.99 0.92 0.83 0.65 0.98 0.82
[19] 0.93 0.81 0.97 0.95 0.70 1.00 0.90 0.99 0.95
[28] 0.95 0.97 1.00 0.99
 Selecting Subsets of Data
> myData$Learning
[1] 0.90 0.87 0.90 0.85 0.93 0.93 0.89 0.80 0.98
[10] 0.88 0.88 0.94 0.99 0.92 0.83 0.65 0.57 0.55
[19] 0.94 0.68 0.89 0.60 0.63 0.84 0.92 0.56 0.78
[28] 0.54 0.47 0.45 0.59 0.91 0.98 0.82 0.93 0.81
[37] 0.97 0.95 0.70 1.00 0.90 0.99 0.95 0.95 0.97
[46] 1.00 0.99 0.18 0.33 0.88 0.23 0.75 0.21 0.35
[55] 0.70 0.34 0.43 0.75 0.44 0.44 0.29 0.48 0.28
> attach(myData)
> Learning
[1] 0.90 0.87 0.90 0.85 0.93 0.93 0.89 0.80 0.98
[10] 0.88 0.88 0.94 0.99 0.92 0.83 0.65 0.57 0.55
[19] 0.94 0.68 0.89 0.60 0.63 0.84 0.92 0.56 0.78
[28] 0.54 0.47 0.45 0.59 0.91 0.98 0.82 0.93 0.81
[37] 0.97 0.95 0.70 1.00 0.90 0.99 0.95 0.95 0.97
[46] 1.00 0.99 0.18 0.33 0.88 0.23 0.75 0.21 0.35
[55] 0.70 0.34 0.43 0.75 0.44 0.44 0.29 0.48 0.28
 Selecting Subsets of Data

> Learning[Group=="A"]
[1] 0.90 0.87 0.90 0.85 0.93 0.93 0.89 0.80 0.98
[10] 0.88 0.88 0.94 0.99 0.92 0.83 0.65 0.98 0.82
[19] 0.93 0.81 0.97 0.95 0.70 1.00 0.90 0.99 0.95
[28] 0.95 0.97 1.00 0.99
> Learning[Group!="A"]
[1] 0.57 0.55 0.94 0.68 0.89 0.60 0.63 0.84 0.92
[10] 0.56 0.78 0.54 0.47 0.45 0.59 0.91 0.18 0.33
[19] 0.88 0.23 0.75 0.21 0.35 0.70 0.34 0.43 0.75
[28] 0.44 0.44 0.29 0.48 0.28
> Condition[Group=="B"&Learning<0.5]
[1] Low Low High High High High High High High
[10] High High High High High
Levels: High Low
 Storing data
• Every R object can be stored into and restored from a file with the commands
“save” and “load”.
• This uses the XDR (external data representation) standard of Sun Microsystems
and others, and is portable between MS-Windows, Unix, Mac.

> save(x, file=“x.Rdata”)

> load(“x.Rdata”)
 Dataframes
• R handles data in objects known as dataframes;
– rows: different observations;
– columns: values of the different variables (numbers,
text, calendar dates or logical variables (T or F);
 Dataframes (II)
• All the values of the same explanatory variables must
go in the same column!
• If you importing data from Excel, save the data in as
tab-delimited text files
• The function read.table will fail if there are spaces in
any of the variable names in the header (row 1) =>
replace “ ” by “.”
• To read dataframes into R:
– path: in double quotes;
– header = T :the first row contains the variables names;
– GUI: Used double back slash \\
> worms<-read.table(“c:\\worms.txt",header=T,row.names=1)
 Dataframes (III)
• Use attach to make the variables accessible by
name:
> attach(worms)
• Use names to get a list of variable names:
> names(worms)
[1] "Area" "Slope" "Vegetation"
"Soil.pH" "Damp"
[6] "Worm.density“
• To see the content of the dataframe (object)
just type ist name:
> worms
 Dataframes (III)
• Summary(worms)
Area Slope Vegetation Soil.pH Damp Worm.density
Min. :0.800 Min. : 0.00 Arable :3 Min. :3.500 Mode :logical Min. :0.00
1st Qu.:2.175 1st Qu.: 0.75 Grassland:9 1st Qu.:4.100 FALSE:14 1st Qu.:2.00
Median :3.000 Median : 2.00 Meadow :3 Median :4.600 TRUE :6 Median :4.00
Mean :2.990 Mean : 3.50 Orchard :1 Mean :4.555 Mean :4.35
3rd Qu.:3.725 3rd Qu.: 5.25 Scrub :4 3rd Qu.:5.000 3rd Qu.:6.25
Max. :5.100 Max. :11.00 Max. :5.700 Max. :9.00

• Values of the continuous variables:

– arithmetic mean;
– maximum, minimum, median, 25 and 75 percentiles
(first and third quartile);
• Levels of categorical variables are counted
 Selecting Parts of a Dataframe: Subscripts

• Subscripts within square brackets: to select part

of a dataframe
• [, means “all the rows” and ,] means “all the
columns”
• To select the first three column of the dataframe
worms:
> worms[,1:3]
Area Slope Vegetation
Nashs.Field 3.6 11 Grassland
Silwood.Bottom 5.1 2 Arable
Nursery.Field 2.8 3 Grassland
Rush.Meadow 2.4 5 Meadow
Gunness.Thicket 3.8 0 Scrub
(…)
 Selecting Parts of a Dataframe: Subscripts (II)

• To select certain rows based on logical tests on the values of one or more
variables:

> worms[Area>3&Slope<3,]

Area Slope Vegetation Soil.pH Damp Worm.density

Silwood.Bottom 5.1 2 Arable 5.2 FALSE 7
Gunness.Thicket 3.8 0 Scrub 4.2 FALSE 6
Oak.Mead 3.1 2 Grassland 3.9 FALSE 2
North.Gravel 3.3 1 Grassland 4.1 FALSE 1
South.Gravel 3.7 2 Grassland 4.0 FALSE 2
Pond.Field 4.1 0 Meadow 5.0 TRUE 6
Water.Meadow 3.9 0 Meadow 4.9 TRUE 8
Pound.Hill 4.4 2 Arable 4.5 FALSE 5
 Value Labels
To understand value labels in R, you need to understand the data structure factor.
You can use the factor function to create your own value lables.
# variable v1 is coded 1, 2 or 3
# we want to attach value labels 1=red, 2=blue,3=green
mydata$v1 <- factor(mydata$v1,
levels = c(1,2,3),
labels = c("red", "blue", "green"))
# variable y is coded 1, 3 or 5
# we want to attach value labels 1=Low, 3=Medium, 5=High
 Value Labels
mydata$v1 <- ordered(mydata$y,
levels = c(1,3, 5),
labels = c("Low", "Medium", "High"))
Use the factor() function for nominal data and the ordered() function
for ordinal data. R statistical and graphic functions will then treat
the data appropriately.
Note: factor and ordered are used the same way, with the same
arguments. The former creates factors and the later creates
ordered factors.
 Missing Data
• In R, missing values are represented by the symbol NA (not
available) . Impossible values (e.g., dividing by zero) are represented
by the symbol NaN (not a number). Unlike SAS, R uses the same
symbol for character and numeric data.
• Testing for Missing Values
• is.na(x) # returns TRUE of x is missing
• y <- c(1,2,3,NA)
• is.na(y) # returns a vector (F F F T)
 Missing Data
• Recoding Values to Missing
– # recode 99 to missing for variable v1
– # select rows where v1 is 99 and recode column v1
– mydata[mydata$v1==99,"v1"] <- NA
• Excluding Missing Values from Analyses
– Arithmetic functions on missing values yield missing values.
– x <- c(1,2,NA,3)
– mean(x) # returns NA
– mean(x, na.rm=TRUE) # returns 2
 Missing Data
• The function complete.cases() returns a logical vector
indicating which cases are complete.
– list rows of data that have missing values
mydata[!complete.cases(mydata),]
• The function na.omit() returns the object with listwise
deletion of missing values.
– create new dataset without missing data
newdata <- na.omit(mydata)
 Date Values
Dates are represented as the number of days since 1970-01-01, with
negative values for earlier dates.
# use as.Date( ) to convert strings to dates
mydates <- as.Date(c("2007-06-22", "2004-02-13"))
# number of days between 6/22/07 and 2/13/04
days <- mydates[1] - mydates[2]
Sys.Date( ) returns today's date.
Date() returns the current date and time.
 Date Values
The following symbols can be used with the format( )
function to print dates.
Symbol Meaning Example

%d day as a number (0-31) 01-31

%a abbreviated weekday Mon

%A unabbreviated weekday Monday

%m month (00-12) 00-12

%b abbreviated month Jan

%B unabbreviated month January

%y 2-digit year 07
%Y 4-digit year 2007
 Date Values
# print today's date
today <- Sys.Date()
format(today, format="%B %d %Y")
"June 20 2007"
Variables, Lists, and Arrays
 Object orientation
primitive (or: atomic) data types in R are:

• numeric (integer, double, complex)

• character
• logical
• function
out of these, vectors, arrays, lists can be built.
 Object orientation
• Object: a collection of atomic variables and/or other objects that
belong together
• Example: a microarray experiment
• probe intensities
• patient data (tissue location, diagnosis, follow-up)
• gene data (sequence, IDs, annotation)

Parlance:
• class: the “abstract” definition of it
• object: a concrete instance
• method: other word for ‘function’
• slot: a component of an object
 Object orientation
Advantages:
Encapsulation (can use the objects and methods someone else has written without having
to care about the internals)
Generic functions (e.g. plot, print)
Inheritance (hierarchical organization of complexity)
Caveat:
Overcomplicated, baroque program architecture…
 Variables
> a = 49
> sqrt(a)
[1] 7
numeric
> a = "The dog ate my homework"
> sub("dog","cat",a)
[1] "The cat ate my homework“
character
> a = (1+1==3) string
>a
[1] FALSE

logical
 Variable Labels
R's ability to handle variable labels is somewhat
unsatisfying.
If you use the Hmisc package, you can take advantage of
some labeling features.
library(Hmisc)
label(mydata$myvar) <- "Variable label for variable
myvar"
describe(mydata)
 Variable Labels
Unfortunately the label is only in effect for functions provided by
the Hmisc package, such as describe(). Your other option is to
use the variable label as the variable name and then refer to
the variable by position index.
names(mydata)[3] <- "This is the label for variable 3"
mydata[3] # list the variable
 Vectors, matrices and arrays
• vector: an ordered collection of data of the same type
> a = c(1,2,3)
> a*2
[1] 2 4 6

• Example: the mean spot intensities of all 15488 spots on a chip: a vector of 15488
numbers

• In R, a single number is the special case of a vector with 1 element.

• Other vector types: character strings, logical
 Vectors, matrices and arrays
• matrix: a rectangular table of data of the same type

• example: the expression values for 10000 genes for 30 tissue biopsies: a matrix with
10000 rows and 30 columns.

• array: 3-,4-,..dimensional matrix

• example: the red and green foreground and background values for 20000 spots on
120 chips: a 4 x 20000 x 120 (3D) array.
Subscripts: Obtaining Parts of Vectors
• Elements of vectors by subscripts in []:
> y[3]
• The third to the seventh elements of y:
> y[3:7]
• The third, fifth, sixth and ninth elements:
> y[c(3,5,6,7)]
• To drop an element from the array, use negative
subscripts:
> y[-1]
• To drop the last element of the array without
knowing its length:
> y[-length(y)]
 Subscripts as Logical Variables
• Logical condition to find a subset of the values
in a vector:
> y[y>6]

• To know the values for z for wich y>6:

> z[y>6]

• Element of y not multiples of three:

> y[y%%3!=0]
 Subscripts with Arrays (I)
• Three-dimensional array containing the numbers 1 to 30, with five rows and three
columns in each two tables:
> A<-array(1:30,c(5,3,2))
> A
, , 1

[,1] [,2] [,3] The numbers enter each table

[1,] 1 6 11 column-wise, from left to right
[2,] 2 7 12 (rows, then columns then tables)
[3,] 3 8 13
[4,] 4 9 14
[5,] 5 10 15

, , 2

[,1] [,2] [,3]

[1,] 16 21 26
[2,] 17 22 27
[3,] 18 23 28
[4,] 19 24 29
[5,] 20 25 30
Subscripts with Arrays (II)
• To select columns of A (e.g. second and third):
> A[,2:3,] : Columns are the second (middle) subscript

, , 1

[,1] [,2]
[1,] 6 11
[2,] 7 12
[3,] 8 13
[4,] 9 14
[5,] 10 15

, , 2

[,1] [,2]
[1,] 21 26
[2,] 22 27
[3,] 23 28
[4,] 24 29
[5,] 25 30
Subscripts with Arrays (III)
• To select columns of A (e.g. second and third) and rows (e.g. two
to four), of only the second table:

> A[2:4,2:3,2] : rows are the first, columns are the second,
and table are the third subscript
[,1] [,2]
[1,] 22 27
[2,] 23 28
[3,] 24 29
 Lists
• vector: an ordered collection of data of the same type.
> a = c(7,5,1)
> a[2]
[1] 5

• list: an ordered collection of data of arbitrary types.

> doe = list(name="john",age=28,married=F)
> doe$name
[1] "john“
> doe$age
[1] 28
• Typically, vector elements are accessed by their index (an integer), list elements by their
name (a character string). But both types support both access methods.
 Installing, Running, and Interacting with R
Math: Variables:
> 1 + 1 > x <- 1
[1] 2 > x
[1] 1
> 1 + 1 * 7 > y = 2
[1] 8 > y
[1] 2
> (1 + 1) * 7 > 3 -> z
[1] 14 > z
[1] 3
> (x + y) * z
[1] 9
 Installing, Running, and Interacting with R
Arrays:
> x <- c(0,1,2,3,4)
> x
[1] 0 1 2 3 4

> y <- 1:5

> y
[1] 1 2 3 4 5

> z <- 1:50

> z
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
[16] 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30
[31] 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45
[46] 46 47 48 49 50
 Installing, Running, and Interacting with R
Math on arrays:
> x <- c(0,1,2,3,4)
> y <- 1:5
> z <- 1:50
> x + y
[1] 1 3 5 7 9
> x * y
[1] 0 2 6 12 20
> x * z
[1] 0 2 6 12 20 0 7 16 27 40 0
[12] 12 26 42 60 0 17 36 57 80 0 22
[23] 46 72 100 0 27 56 87 120 0 32 66
[34] 102 140 0 37 76 117 160 0 42 86 132
[45] 180 0 47 96 147 200
 Functions

> arc <- function(x) 2*asin(sqrt(x))

> arc(0.5)
[1] 1.570796
> x <- c(0,1,2,3,4)
> x <- x / 10
> arc(x)
[1] 0.0000000 0.6435011 0.9272952
[4] 1.1592795 1.3694384

> plot(arc(Percents)~Percents,
+ pch=21,cex=2,xlim=c(0,1),ylim=c(0,pi),
+ main="The Arcsine Transformation")
> lines(c(0,1),c(0,pi),col="red",lwd=2)
 R Packages
– One of the strengths of R is that the system can easily be
extended. The system allows you to write new functions
and package those functions in a so called `R package' (or
`R library'). The R package may also contain other R
objects, for example data sets or documentation. There is
a lively R user community and many R packages have been
written and made available on CRAN for other users. Just
a few examples, there are packages for portfolio
optimization, drawing maps, exporting objects to html,
time series analysis, spatial statistics and the list goes on
and on.
 R Packages
– To attach another package to the system you can use the menu or the
library function. Via the menu:

Select the `Packages' menu and select `Load package...', a list of available
packages on your system will be displayed. Select one and click `OK', the
package is now attached to your current R session. Via the library function:

> library(MASS)
> shoes
$A
[1] 13.2 8.2 10.9 14.3 10.7 6.6 9.5 10.8 8.8 13.3
$B
[1] 14.0 8.8 11.2 14.2 11.8 6.4 9.8 11.3 9.3 13.6
Data Manipulation
 Outline
• Creating New Variable
• Operators
• Built-in functions
• Control Structures
• User Defined Functions
• Sorting Data
• Merging Data
• Aggregating Data
• Reshaping Data
• Sub-setting Data
• Data Type Conversions
 Introduction

Once you have access to your data, you will want to

massage it into useful form. This includes creating
new variables (including recoding and renaming
existing variables), sorting and merging datasets,
aggregating data, reshaping data, and subsetting
datasets (including selecting observations that
meet criteria, randomly sampling observation, and
dropping or keeping variables).
 Introduction

Each of these activities usually involve the use of R's

built-in operators (arithmetic and logical) and
functions (numeric, character, and statistical).
Additionally, you may need to use control
structures (if-then, for, while, switch) in your
programs and/or create your own functions. Finally
you may need to convert variables or datasets from
one type to another (e.g. numeric to character or
matrix to dataframe).
Creating new variables
• Use the assignment operator <- to create new variables. A
wide array of operators and functions are available here.
• # Three examples for doing the same computations
mydata$sum <- mydata$x1 + mydata$x2
mydata$mean <- (mydata$x1 + mydata$x2)/2
attach(mydata)
mydata$sum <- x1 + x2
mydata$mean <- (x1 + x2)/2
detach(mydata)
• mydata <- transform( mydata,
sum = x1 + x2,
mean = (x1 + x2)/2
)
Creating new variables
Recoding variables
• In order to recode data, you will probably use one or
more of R's control structures.
• # create 2 age categories
mydata$agecat <- ifelse(mydata$age > 70,
c("older"), c("younger"))
# another example: create 3 age categories
attach(mydata)
mydata$agecat[age > 75] <- "Elder"
mydata$agecat[age > 45 & age <= 75] <- "Middle Aged"
mydata$agecat[age <= 45] <- "Young"
detach(mydata)
Creating new variables
Recoding variables
• In order to recode data, you will probably use one or more of
R's control structures.
• # create 2 age categories
mydata$agecat <- ifelse(mydata$age > 70,
c("older"), c("younger"))

# another example: create 3 age categories

attach(mydata)
mydata$agecat[age > 75] <- "Elder"
mydata$agecat[age > 45 & age <= 75] <- "Middle Aged"
mydata$agecat[age <= 45] <- "Young"
detach(mydata)
Creating new variables
Renaming variables
• You can rename variables programmatically or interactively.
• # rename interactively
fix(mydata) # results are saved on close

# rename programmatically
library(reshape)
mydata <- rename(mydata, c(oldname="newname"))

# you can re-enter all the variable names in order

# changing the ones you need to change.the limitation
# is that you need to enter all of them!
names(mydata) <- c("x1","age","y", "ses")
Arithmetic Operators
Operator Description
+ addition
- subtraction
* multiplication
/ division
^ or ** exponentiation
x %% y modulus (x mod y) 5%%2 is 1
x %/% y integer division 5%/%2 is 2
 Logical Operators
Operator Description
< less than
<= less than or equal to
> greater than
>= greater than or equal to
== exactly equal to
!= not equal to
!x Not x
x|y x OR y
x&y x AND y
isTRUE(x) test if x is TRUE
 Control Structures

• R has the standard control structures you would

expect. expr can be multiple (compound)
statements by enclosing them in braces { }. It is
more efficient to use built-in functions rather than
control structures whenever possible.
 Control Structures
• if-else
• if (cond) expr
if (cond) expr1 else expr2
• for
• for (var in seq) expr
• while
• while (cond) expr
• switch
• switch(expr, ...)
• ifelse
• ifelse(test,yes,no)
 Control Structures
• # transpose of a matrix
# a poor alternative to built-in t() function
mytrans <- function(x) {
if (!is.matrix(x)) {
warning("argument is not a matrix: returning NA")
return(NA_real_)
}
y <- matrix(1, nrow=ncol(x), ncol=nrow(x))
for (i in 1:nrow(x)) {
for (j in 1:ncol(x)) {
y[j,i] <- x[i,j]
}
}
return(y)
}
 Control Structures
• # try it
z <- matrix(1:10, nrow=5, ncol=2)
tz <- mytrans(z)
R built-in functions

Almost everything in R is done through

functions. Here I'm only referring to
numeric and character functions that
are commonly used in creating or
recoding variables.

Note that while the examples on this

page apply functions to individual
variables, many can be applied to
vectors and matrices as well.
Numeric Functions
Function Description
abs(x) absolute value
sqrt(x) square root
ceiling(x) ceiling(3.475) is 4
floor(x) floor(3.475) is 3
trunc(x) trunc(5.99) is 5
round(x, digits=n) round(3.475, digits=2) is 3.48
signif(x, digits=n) signif(3.475, digits=2) is 3.5
cos(x), sin(x), tan(x) also acos(x), cosh(x), acosh(x), etc.
log(x) natural logarithm
log10(x) common logarithm
exp(x) e^x
 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")
paste("Today is", date())

toupper(x) Uppercase
tolower(x) Lowercase
Stat/Prob Functions
• The following table describes functions related to
probaility distributions. For random number
generators below, you can use set.seed(1234) or
some other integer to create reproducible pseudo-
random numbers.
Function Description
dnorm(x) normal density function (by default m=0 sd=1)
# plot standard normal curve
x <- pretty(c(-3,3), 30)
y <- dnorm(x)
plot(x, y, type='l', xlab="Normal Deviate", ylab="Density", yaxs="i")
pnorm(q) cumulative normal probability for q
(area under the normal curve to the right of q)
pnorm(1.96) is 0.975
qnorm(p) normal quantile.
value at the p percentile of normal distribution
qnorm(.9) is 1.28 # 90th percentile
rnorm(n, m=0,sd=1) n random normal deviates with mean m
and standard deviation sd.
#50 random normal variates with mean=50, sd=10
x <- rnorm(50, m=50, sd=10)
dbinom(x, size, prob) binomial distribution where size is the sample size
pbinom(q, size, prob) and prob is the probability of a heads (pi)
qbinom(p, size, prob) # prob of 0 to 5 heads of fair coin out of 10 flips
rbinom(n, size, prob) dbinom(0:5, 10, .5)
# prob of 5 or less heads of fair coin out of 10 flips
pbinom(5, 10, .5)
dpois(x, lamda) poisson distribution with m=std=lamda
ppois(q, lamda) #probability of 0,1, or 2 events with lamda=4
qpois(p, lamda) dpois(0:2, 4)
rpois(n, lamda) # probability of at least 3 events with lamda=4
1- ppois(2,4)
dunif(x, min=0, max=1) uniform distribution, follows the same pattern
punif(q, min=0, max=1) as the normal distribution above.
qunif(p, min=0, max=1) #10 uniform random variates
runif(n, min=0, max=1) x <- runif(10)
Function Description

mean(x, trim=0, mean of object x

na.rm=FALSE) # trimmed mean, removing any missing values and
# 5 percent of highest and lowest scores
mx <- mean(x,trim=.05,na.rm=TRUE)

sd(x) standard deviation of object(x). also look at var(x) for variance and mad(x) for median absolute
deviation.

median(x) median

quantile(x, probs) quantiles where x is the numeric vector whose quantiles are desired and probs is a numeric vector with
probabilities in [0,1].
# 30th and 84th percentiles of x
y <- quantile(x, c(.3,.84))

range(x) range

sum(x) sum

diff(x, lag=1) lagged differences, with lag indicating which lag to use

min(x) minimum

max(x) maximum

scale(x, center=TRUE, column center or standardize a matrix.

scale=TRUE)
Other Useful Functions

Function Description

seq(from , to, by) generate a sequence

indices <- seq(1,10,2)
#indices is c(1, 3, 5, 7, 9)

rep(x, ntimes) repeat x n times

y <- rep(1:3, 2)
# y is c(1, 2, 3, 1, 2, 3)

cut(x, n) divide continuous variable in factor with n levels

y <- cut(x, 5)
 Sorting
• To sort a dataframe in R, use the order( ) function. By default,
sorting is ASCENDING. Prepend the sorting variable by a
minus sign to indicate DESCENDING order. Here are some
examples.
• # sorting examples using the mtcars dataset
data(mtcars)
# sort by mpg
newdata = mtcars[order(mtcars$mpg),]
# sort by mpg and cyl
newdata <- mtcars[order(mtcars$mpg, mtcars$cyl),]
#sort by mpg (ascending) and cyl (descending)
newdata <- mtcars[order(mtcars$mpg, -mtcars$cyl),]
 Merging
To merge two dataframes (datasets) horizontally, use the merge
function. In most cases, you join two dataframes by one or
more common key variables (i.e., an inner join).
# merge two dataframes by ID
total <- merge(dataframeA,dataframeB,by="ID")
# merge two dataframes by ID and Country
total <- merge(dataframeA,dataframeB,by=c("ID","Country"))
 Merging
ADDING ROWS
To join two dataframes (datasets) vertically, use the rbind
function. The two dataframes must have the same variables,
but they do not have to be in the same order.
total <- rbind(dataframeA, dataframeB)

If dataframeA has variables that dataframeB does not, then either:

Delete the extra variables in dataframeA or
Create the additional variables in dataframeB and set them to NA (missing)
before joining them with rbind.
 Aggregating
• It is relatively easy to collapse data in R using one
or more BY variables and a defined function.
• # aggregate dataframe mtcars by cyl and vs,
returning means
# for numeric variables
attach(mtcars)
aggdata <-aggregate(mtcars, by=list(cyl),
FUN=mean, na.rm=TRUE)
print(aggdata)
• OR use apply
 Aggregating
• When using the aggregate() function, the by
variables must be in a list (even if there is only
one). The function can be built-in or user
provided.
• See also:
• summarize() in the Hmisc package
• summaryBy() in the doBy package
 Data Type Conversion
• Type conversions in R work as you would expect.
For example, adding a character string to a
numeric vector converts all the elements in the
vector to character.
• Use is.foo to test for data type foo. Returns TRUE
or FALSE
Use as.foo to explicitly convert it.
• is.numeric(), is.character(), is.vector(), is.matrix(),
is.data.frame()
as.numeric(), as.character(), as.vector(),
as.matrix(), as.data.frame)