Tutorial Using R (and RStudio)

1 INTRODUCTION TO STATISTICS

Statistics is the science of learning from data. It is the fields that deal with all aspect of data
including the planning of data collection, data preparation, analysis and interpretation to
make credible understanding or meaning from data in making more effective decisions. In
general, there are two types of statistics:
Descriptive statistics: statistics that summarize, organize and make sense of
observations. In other word, descriptive statistics is concerned to describe certain
features of a variable.
Inferential statistics: statistics use data gathered from a sample to make inferences about
the larger population from which the sample was drawn.

1.1 Basic terms

Population consists of all items or elements of interest for a particular decision or

investigation. Example: all married staff over the age of 25 in UTeM.
Sample is a certain number of elements that have been chosen from a population. Sample
is a subset of population. Example: a list of married staffs over the age of 25 in the
Registrars Office would be a sample from the population of all married staff over the age
of 25 in the UTeM.
Variable is a characteristic of the individual within the sample or population.
Observation/Measurement is the value of a variable for an element.
Data set is a collection of values of one or more variables.
Raw data is data recorded in the sequence in which they are collected and before they
are processed or ranked.
Outliers / Extreme Values are values that are very small or very large relative to the
majority of the values in a data set.
2 Introduction to Statistics

1.2 Variable

In statistics, each variable is required to be defined and categorized with the scales of
measurement. Each scale of measurement has certain properties which in turn determine the
appropriateness for use of certain statistical analyses. The four scales of measurement are
nominal, ordinal, interval, and ratio.

Nominal ( Qualitative)

Categorical data and numbers that are simply used as identifiers or names represent a nominal
scale of measurement. Each observation belongs to some distinctively different categories. It is
cannot be quantified or ranked. (i.e. 1=Married, 2=Single ; M=Married, S=Single)

Ordinal: (Quantitative)

An ordinal scale of measurement represents an ordered series of relationships or rank order.

Fundamentally, these scales do not represent a measurable quantity. For example, individuals
competing in a contest may be fortunate to achieve first, second, or third place. Likert-type scales
(such as "On a scale of 1 to 10, with one being no pain and ten being high pain, how much pain
are you in today?") also represent ordinal data.

Interval: ( Quantitative)

A scale that represents quantity and has equal units but for which zero represents simply an
additional point of measurement is an interval scale. The Fahrenheit scale is a clear example of
the interval scale of measurement. Thus, 60 degree Fahrenheit or -10 degrees Fahrenheit
represent interval data. Measurement of Sea Level is another example of an interval scale. With
each of these scales there are direct, measurable quantities with equality of units. In addition,
zero does not represent the absolute lowest value. Rather, it is point on the scale with numbers
both above and below it (for example, -10degrees Fahrenheit).

Ratio: ( Quantitative)

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3 Introduction to Statistics

The ratio scale of measurement is similar to the interval scale in that it also represents quantity
and has equality of units. However, this scale also has an absolute zero (no numbers exist below
zero). Very often, physical measures will represent ratio data (for example, height and weight). If
one is measuring the length of a piece of wood in centimeters, there is quantity, equal units, and
that measure cannot go below zero centimeters. A negative length is not possible.

The table can be used to conduct descriptive statistics between the four scales of measurement

Table 1.1 Descriptive statistic

Qualitative Quantitative

[Nominal] [Ordinal ] [Interval/ratio]

Unordered
Definition Ordered Categories Numeric Values
Categories

Satisfaction Level, Age

Examples State Code, Gender Income, Age
Group

Central Tendency Mode Mode / Median Mode / Median / Mean

Min / Max / IQR /

Dispersion Min / Max / IQR / Range
Range / Std. Dev

Histogram (with
Graph Pie / Bar Pie / Bar
normal curve)

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4 Introduction to R

2 INTRODUCTION TO R
R is widely known as a free software programming language and software environment
for statistical computing and graphics. It provides a wide variety of statistical analysis such as
linear and nonlinear modelling, time-series analysis, classical statistical tests, and graphical
techniques which is highly extensible. Likewise, R is also an integrated suite of software which
facilities data manipulation, calculation and graphical display. The functionalities of R includes
an effective data handling and storage facility, a suite of operators for calculations, integrated
collection of intermediate tools for data analysis, graphical facilities for data analysis as well as a
well-developed, simple yet effective programming language which includes conditionals, loops,
user-defined recursive functions and input and output facilities.
There are around eight packages supplied with the R. Those packages are available through the
Comprehensive R Archives Network (CRAN) sites, http://cran.stat.nus.edu.sg. The
functionalities are quite similar as Minitab, SPSS and other statistical software that we can find
in the market. However, this R is almost similar like a Matlab which it allows us to do
programming in order to do computation and generate graphical view (graph).

2.1 Motivation to Use R

R is the most preferable software because of:

It is free
Leading developers of statistical software are writing functions for this package. Thus
competency in R means we can stay up to date with statistics.
It covers statistical applications from the simplest to the complex and would allow us to
complete all our statistical training using R.
R covers different topics in a consistent way so that the programming we learn for say
linear models will also be done the same way for non-linear models. This consistency is
convenient to statistical modelling.
R has a powerful suite of functions that allow you to use modern statistical methods.
Modern statistics has simplified many problems through the use of graphics and
computer intensive ideas.

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5 Introduction to R

It involves the biggest concentration of statisticians worldwide. So it can be accessed to

the best and most efficient methods used by R clients worldwide.

2.2 The background of R package

R is an open-source package for statistical computing. Open source has a number of different
meanings; here the important one is that R is freely available, and its users are free to see how it
is written, and to improve it. R is based on the computer language S, developed by John
Chambers and others at Bell Laboratories in 1976. In 1993 Robert Gentleman and Ross Ihaka at
the University of Auckland wanted to do experiment with the language, so they developed an
implementation, and named it R. They made it open source in 1995, and hundreds of people
around the world have contributed to its development until today.
S-PLUS is a commercial implementation of the S language. Because both R and S-PLUS are
based on the S language, much of what is described in what follows will apply without change to
S-PLUS. However, other statistical packages such as S-PLUS, SAS, SPSS are not free. These are
the licensed software and we have to buy in the market.

2.3 Installation of R

R can be downloaded from http://www.r-project.org/ by following these steps:

Browse http://www.r-project.org/

Click download R

Go to Singapore website => http://cran.stat.nus.edu.sg/. The software can be obtained

from National University of Singapore

We can download the software depends on our operating system

Download R for Linux or Download R for (Mac) OS X or Download R for Windows

Go to install R for the first time.

We can read the available information and most frequent asked questions in the website.

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6 Introduction to R

Click Download R-3.1.0 for Windows and save into our hard disk (will take some time as
the file is big, 54MB for 32/64 bit machines).

Run R-3.1.0 - window installation file

Follow all instruction until finish.

2.4 Starting and Quitting R

2.4.1 Syntax of R

In Microsoft Windows, the R installer will have created a start menu item and an icon for R on
our desktop. Double clicking on the R icon to start the program.

From the start menu we can go to All Programs => R => R.

First thing that will happen is that R will open the console, into which the user can type any
commands. The greater-than sign (>) is the prompt symbol. When this appears, you can begin
typing commands.

2.4.2 Simple mathematical calculation

R can be used as a calculator. For example, Simple arithmetic expression:

> 5 + 49

Upon pressing the Enter key, the result 54 appears, prefixed by the number 1 in square brackets:
> 5 + 49
[1] 54
The [1] indicates that this is the first (and in
this case only) result from the command
The sequence of integers from 1 to 100 may be displayed as follows:
> 1:100

You can set the width for better view of data.

> options(width=40)
> 1:100

Multiplication symbol is "*"

>3*5
[1] 15

Comment

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Sign "#" is used for any remark and comment. Everything following a "#" sign is assumed to be a ignored
by R.
> # type any comment and the comment is ignored by R

More calculation
>3-8
[1] -5
> 12 / 4
[1] 3
> 13 / 5
[1] 2.6 Note what happens if you omit the parentheses () when attempting
to quit:
>q
2.4.3 Quit From R function (save = "default", status = 0, runLast = TRUE)
To quit your R session, type .Internal(quit(save, status, runLast))
> q() <environment: namespace:base>

This has happened because q is a function that is used to tell R to quit.

Typing q by itself tells R to show us the (not very pleasant-looking)
contents of the function q. By typing q(), we are telling R to call the
function q. The action of this function is to quit R. Everything that R does is
done through calls to functions.

3 INTRODUCTION TO RSTUDIO

The RStudio IDE is a user interface for R. Its free and open source, and works on Windows,
Mac, and Linux. RStudio is not a replacement for R. R must be installed in addition to RStudio.
However, when both are installed on your system, only RStudio needs to be run.

R STUDIO INSTALLATION .

R Studio installation is straightforward as follows:

i) Go to http://www.rstudio.com/
ii) Go to Powerful IDE for R
iii) Click download now

iv) If you run R on your desktop, click

v) Download RStudio 0.98.507 - Windows XP/Vista/7/8 35.4Mb (depends on your OS)
vi) Run the installation file until finish.

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8 Introduction to RStudio

Start > All programs > RStudio>RStudio

3.1 RStudio layout

The RStudio interface consists of several main windows sitting below a top-level toolbar and
menu bar. Although this placement can be adjusted, the default layout utilizes four main panels
or panes in the following positions:

Position Panels Function

Top left Source window for editing files or viewing some data sets.
Bottom left Console window The console is where you can type
commands and see output
Top right Workspace/history window to hold a Workspace browser and History

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9 Introduction to RStudio

browser. The workspace tab stores any object,

value, function or anything you create during
your R session. In the example below, if you
click on the dotted squares you can see the data
on a screen to the left.
The history tab keeps a record of all previous
commands. It helps when testing and running
processes. Here you can either save the whole
list or you can select the commands you want
and send them to an R script to keep track of
your work.
Bottom right Files/plot/packages/help to hold tabs for interacting with the Files, Plots,
window Packages, and Help system components .

3.2 Changing the working directory

If you have different projects you can change the working directory for that session, see above.
Or you can type:

# Shows the working directory (wd)

getwd()

# Changes the wd

setwd("C:/myfolder/data")

3.3 Starting new project

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10 Introduction to RStudio

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11 Introduction to RStudio

Click > Empty Project

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13 Introduction to RStudio

3.4 Entering Data & Analysis

The easiest way to enter data in R is to work with a text file, in which the columns are
separated by tabs. There are many ways in which you can get such files. Here we simply
explain how to make such a file with Excel. Open Excel and enter the data.

3.4.1 Quantitative data

Example 1: Students marks

After enter the data in worksheet in Excel, give the file a name (e.g. student) and select the
option Text (Tab delimited). Now save the file.

To enter the data in RStudio you can use the command Import Dataset from Text File:

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Find the student.txt file and open it. Import the data as shown in the following screenshot:

Now you have defined a dataset in R, called student, containing the variable midMarks as shown
in source window (upper left panel).

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15 Introduction to RStudio

3.5 Simple Statistical Analysis

To start analyzing, create the workspace with a new Rscript file (click on the option File or
create icon in the menu bar)

To make sure you have entered your data correctly, type the command list (student),
activate it (by going over it with the mouse, while you keep the left button pressed and click on
Run Line(s).

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16 Introduction to RStudio

This should show you the data of the midmarks in the lower left panel.

3.5.1 Running simple analysis

Two of the most common statistics are the mean and standard deviation:

Mean : #Simple statistic

## remember to send to object and

access the data to the column by
typing the table name and
followed by a dollar sign $
Variance : Mystud=Student$Mid_marks
mean(mystud)
summary(mystud)
sd(mystud)

Standard Deviation :

= square root Variance S2

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17 Introduction to RStudio

3.5.2 Creating the graph

Histogram

> hist(mystud)

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18 Descriptive Statistics

Boxplot

>boxplot (mystud, main="The Mid-term marks", ylab=" marks" )

4 DESCRIPTIVE STATISTICS
4.1 Frequency

#simple frequency

x=table(mystud)
x
barplot (x)

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4.2 More Frequency

group=seq(0,100, by=20)
group.data=cut(student$midMarks,group,right=FALSE)
group.data
group.feq=table(group.data)
list(group.feq)
cbind(group.feq)

barplot(group.feq)
barplot(group.feq, col=c("lightblue", "mistyrose",
"lightcyan","lavender", "cornsilk"), )
barplot(group.feq, col=c("lightblue", "mistyrose",
"lightcyan","lavender", "cornsilk"), main= list("Carry mark
BACS1111", font=2))
Making a frequency distribution table at first sight looks more complicated in R than in other
programs. The reason for this, however, is that you use the same commands for the simplest
table as for the more complicated. So, the commands are slightly harder to start with, but
remain the same to make all types of tables, included grouped frequency distribution tables.

First, you have to define the spans you are interested in. Suppose we are interested in all spans
from 0 to 100. This is defined by the command:
group=seq(0,100, by=10)

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20 Descriptive Statistics

This commands defines the lower values of the intervals as the sequence of values from 0 to
100 with a step function of 10 (i.e., it will go from 0 to 10, to 20, etc.). If we define by=20,
then the lower values of the spans will go from 0 to 20, to 40, and so on, which means that we
will have a grouped frequency distribution table.

Next we segment the continuum of values in midMarks according to the spans we defined
above. We do this with the following command:
group.data=cut(student$midMarks,group,right=FALSE)

This commands cuts the values of the variable midMarks data from the dataset student into
parts starting with the lower value defined in span, and ending with the upper value
immediately below the lower value of the next span, and puts it into a new variable group,data.
The following parts are important:
group.data

This is the variable group.data from the dataset student. Variables from a dataset are defined as
dataset$variable (i.e., with a $ sign between the name of the dataset and the name of the
variable).

Span refers to the lower values of the intervals we defined above.

right=FALSE makes that the lower value of the next interval will be excluded from the present
interval. If we had not done this, the interval 20 40 would exclude the number 20 and include
the number 40. Now the interval goes from 20.0 to 39.9999.

To calculate the frequencies of the intervals (Midterm group) we use the command:
group.feq=table(group.data)

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21 Descriptive Statistics

Try change the code > group.data=cut(student$midMarks,group,right=TRUE) and see the

difference.

Saving your script ( eg. Scale.R)

4.3 Quantitative Variable

4.3.1 Entering data

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Write command:

list(student)

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4.3.2 Descriptive Statistics-frequency

##access to the column gender

gen =c(student$gender)
gen

gen.feq=table(student$gender)
gen.feq
cbind(gen.feq)
barplot (gen.feq, col=c("red", "blue"))

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4.4 Quantitative variable (Ordinal)

4.4.1 Entering

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25 Descriptive Statistics

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26 Descriptive Statistics

4.4.2 Descriptive statistics-frequency

List(student)
AssignDiff =c(student$diffAssign)
AssignDiff

#
AssignDiff.feq=table (student$diffAssign)
AssignDiff.feq
cbind(AssignDiff.feq)
pie(AssignDiff.feq)

More advance figure or graph 3D graph .

Try write > pie3D(AssignDiff.feq)

What will you get? Error: could not find function "pie3D"

4.5 Install the package

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27 Descriptive Statistics

In order to have 3D pie, you need to install the package plotrix

Click on Packages tab and checked the plotrix library

The code > library("plotrix", lib.loc="C:/Program Files/R/R-3.0.0/library")

will appear in console window that indicate function Plotrix in your RStudio.

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Write the following code :

pie3D(AssignDiff.feq)
lbls=paste(names (AssignDiff.feq))
pie3D(AssignDiff.feq)
pie3D(AssignDiff.feq, labels=lbls, explode=0.1, main= "Difficulty
level for Assignment")

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29 Inferential Analysis

5 INFERENTIAL ANALYSIS

5.1 Introduction

In terms of inferential statistics R has many varieties of functions for doing statistical analyses
including the parametric and non-parametric t-test, analysis of variance, t-test, correlation and
linear regression.

i. Compare mean using T-test ( Parametric)

Some of them are self-understanding, and really easy to use. This is the case for example to
perform a t-test to compare one average value with zero or two average values. The function
t.test() do this. With one argument, the function tests if the average value of the variable
differs from zero. With two arguments it simply compares the two average values, e.g.
t.test(midMarks,finalMarks).

ii. Compare mean Using Wilcoxon rank test ( non-parametric)

The function wilcox.test()performs wilcoxon rank test, which assumes that the means of
two unnormally distributed datasets are equal.

iii. Binomial test

The function binom.test() performs an exact test of a simple null hypothesis about the
probability of success in a percentage. For example, among 125 insects counted, 45 are females,
and we want to see whether this differs from 50% females. For this, binom.test(45,125,.5)
give the corresponding results (the answer is yes, with p= 0.002226).

iv. Kruskal-Wallis rank sum test

The function kruskal.test()performs a Kruskal-Wallis rank sum test of the null that the
location parameters of the distribution of x are the same in each group (sample). The alternative
is that they differ in at least one. It can take a single argument that is either a table with several

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columns corresponding to variables, or else a list() function regrouping all independent

variables in one object as shown below:

## Hollander & Wolfe (1973), 116.

## Mucociliary efficiency from the rate of removal of dust in normal
## subjects, subjects with obstructive airway disease, and subjects
## with asbestosis.
x <- c(2.9, 3.0, 2.5, 2.6, 3.2) # normal subjects
y <- c(3.8, 2.7, 4.0, 2.4) # with obstructive airway disease
z <- c(2.8, 3.4, 3.7, 2.2, 2.0) # with asbestosis
kruskal.test(list(x, y, z))
## Equivalently,
x <- c(x, y, z)
g <- factor(rep(1:3, c(5, 4, 5)),
labels = c("Normal subjects",
"Subjects with obstructive airway disease",
"Subjects with asbestosis"))
kruskal.test(x, g)

## Formula interface.
require(graphics)
boxplot(Ozone ~ Month, data = airquality)
kruskal.test(Ozone ~ Month, data = airquality)

v. Correlation

The function cor.test() tests the correlation or relationship between two vectors, e.g.,
cor.test(midMarks,finalMarks).

Overall, there are several other functions in R, covering (almost) all standard statistical methods.
See http://www.statmethods.net/stats/ttest.html

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5.2 Entering Data

5.3 Compare mean analysis

5.3.1 T-test

list(student)
midterm.data<-c(student$midMarks)
midterm.data
final.data<-c(student$finalMarks)
final.data
t.test(midterm.data,final.data) # independent t-test
t.test(midterm.data,final.data, paired=TRUE) #paired sample t-test
t.test(final.data, mu=75) #Ho:mu=75 #One sample t-test.

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5.3.2 Non-parametric t-test: Wilcoxon rank test

If we are assuming the data to have not normal distribution or small sample size. In our case
n<20, so we can proceed with the non-parametric t-test or Wilcoxon rank test .

wilcox.test(midterm.data,final.data, paired=TRUE)

5.4 Exercises

Exercise 1: A company has proposed a new packaging training and wants to test the
effectiveness of the training by comparing the average times of 10 workers in the packaging
process. The table below shows the time in minute before and after training for each worker.

Before new 12.9, 13.5, 12.8, 15.6, 17.2, 19.2, 12.6, 15.3, 14.4, 11.3
training
After new 12.7, 13.6, 12.0, 15.2, 16.8, 20.0, 12.0, 15.9, 16.0, 11.1
taraining

Answer:

In this case we have two sets of paired samples, since the measurements were made on the same
worker before and after the training. To see if there was an improvement, deterioration, or if the
means of times have remained substantially the same (hypothesis H0), we need to make a
Student's t-test for paired samples, proceeding in this way:

a = c(12.9, 13.5, 12.8, 15.6, 17.2, 19.2, 12.6, 15.3, 14.4, 11.3)
b = c(12.7, 13.6, 12.0, 15.2, 16.8, 20.0, 12.0, 15.9, 16.0, 11.1)

t.test(a,b, paired=TRUE)

Paired t-test

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data: a and b
t = -0.2133, df = 9, p-value = 0.8358
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-0.5802549 0.4802549
sample estimates:
mean of the differences
-0.05

The p-value is greater than 0.05, then we can accept the hypothesis H0 of equality of the
averages. In conclusion, the new training has not made any significant improvement (or
deterioration) to the team of workers.

Exercise 2:
An investigator believes that caffeine facilitates performance on a simple spelling test. Two
groups of subjects are given either 200 mg of caffeine or a placebo. The data are:

Placebo Drug
24 24
25 29
27 26
26 23
26 25
22 28
21 27
22 24
23 27
25 28
25 27
25 26

Answer:

To describe the differences between these two groups, we can use basic descriptive statistics
(means and standard deviations), and graph the results. To see how likely a difference of this

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34 References:

magnitude would happen by chance if, in fact, the two groups were sampled from the same
population, we can do a t-test. Please try

Other exercises:

t-test example: http://www.r-bloggers.com/paired-students-t-test/

non parametric test :http://www.r-bloggers.com/wilcoxon-signed-rank-test/

6 REFERENCES:
For more information on RStudio, try the following resources:

Visit the RStudio homepage, http://www.rstudio.com/ . The site includes a variety of

helpful resources, including the Online learning to learn how to write the R code . The
support websites are available at http://blog.rstudio.org/ and http://www.r-bloggers.com/.
More detailed RStudio help can be found in Getting Started with RStudio.

Other websites:

http://www.statmethods.net/graphs/bar.html
http://www.r-bloggers.com/
https://sites.google.com/site/r4statistics/popularity
http://en.freestatistics.info/
http://lib.stat.cmu.edu/
http://www.comfsm.fm/~dleeling/statistics/notes000.html

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35 Appendix

7 APPENDIX
In RStudio

In SPSS

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