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R Data Mining
Andrea Cirillo
BIRMINGHAM - MUMBAI
R Data Mining
Copyright © 2017 Packt Publishing
All rights reserved. No part of this book may be reproduced, stored in a retrieval system, or
transmitted in any form or by any means, without the prior written permission of the
publisher, except in the case of brief quotations embedded in critical articles or reviews.
Every effort has been made in the preparation of this book to ensure the accuracy of the
information presented. However, the information contained in this book is sold without
warranty, either express or implied. Neither the author, nor Packt Publishing, and its
dealers and distributors will be held liable for any damages caused or alleged to be caused
directly or indirectly by this book.
Packt Publishing has endeavored to provide trademark information about all of the
companies and products mentioned in this book by the appropriate use of capitals.
However, Packt Publishing cannot guarantee the accuracy of this information.
ISBN 978-1-78712-446-2
www.packtpub.com
Credits
Author Copy Editors
Andrea Cirillo Safis Editing
Vikrant Phadkay
Andrea has previously authored RStudio for R Statistical Computing Cookbook for Packt
Publishing.
Enrico has gained more than 10 years of experience with R and other statistical software
training and consulting activities, with a special focus on Six Sigma, industrial statistical
analysis, and corporate training courses. He is also a partner of the main company
supporting the MilanoR Italian community. In this company, he works as a freelance
principal data scientist, as well as teacher of statistical models and data mining with R
training courses.
In his first job, Enrico collaborated with Italian medical institutions, contributing to some
regional projects/publications on nosocomial infections. His main expertise is in consulting
and teaching statistical modeling, data mining, data science, medical statistics, predictive
models, SPC, and industrial statistics. Enrico planning to develop an Italian-language
website dedicated to R (www.r-project.it).
I would like to thank all the people who support me and my activities, particularly my
partner, Sonja, and her son, Gianluca.
Doug Ortiz is an enterprise cloud, big data, data analytics, and solutions architect who has
been architecting, designing, developing, and integrating enterprise solutions throughout
his career. Organizations that leverage his skillset have been able to rediscover and reuse
their underutilized data via existing and emerging technologies such as Amazon Web
Services, Microsoft Azure, Google Cloud, Microsoft BI Stack, Hadoop, Spark, NoSQL
databases, and SharePoint along with related toolsets and technologies.
I would like to thank my wonderful wife, Mila, for all her help and support, as well as
Maria, Nikolay, and our wonderful children.
Radovan Kavicky is the principal data scientist and president at GapData Institute, based in
Bratislava, Slovakia, where he harnesses the power of data and wisdom of economics for
public good. He is a macroeconomist by education, and consultant and analyst by
profession (8+ years of experience in consulting for clients from the public and private
sector), with strong mathematical and analytical skills. He is able to deliver top-level
research and analytical work. From MATLAB, SAS, and Stata, he switched to Python, R and
Tableau.
Radovan is an evangelist of open data and a member of the Slovak Economic Association
(SEA), Open Budget Initiative, Open Government Partnership, and the global Tableau
#DataLeader network (2017). He is the founder of PyData Bratislava, R <- Slovakia, and the
SK/CZ Tableau User Group (skczTUG). He has been a speaker at @TechSummit (Bratislava,
2017) and @PyData (Berlin, 2017).
Oleg Okun is a machine learning expert and author/editor of four books, numerous journal
articles, and many conference papers. His career spans more than a quarter of a century. He
was employed in both academia and industry in his mother country, Belarus, and abroad
(Finland, Sweden, and Germany). His work experience includes document image analysis,
fingerprint biometrics, bioinformatics, online/offline marketing analytics, credit scoring
analytics, and text analytics.
He is interested in all aspects of distributed machine learning and the Internet of Things.
Oleg currently lives and works in Hamburg, Germany.
I would like to express my deepest gratitude to my parents for everything that they have
done for me.
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Table of Contents
Preface 1
Chapter 1: Why to Choose R for Your Data Mining and Where to Start 6
What is R? 7
A bit of history 8
R's points of strength 8
Open source inside 8
Plugin ready 9
Data visualization friendly 10
Installing R and writing R code 12
Downloading R 12
R installation for Windows and macOS 13
R installation for Linux OS 14
Main components of a base R installation 14
Possible alternatives to write and run R code 15
RStudio (all OSs) 16
The Jupyter Notebook (all OSs) 18
Visual Studio (Windows users only) 18
R foundational notions 19
A preliminary R session 20
Executing R interactively through the R console 21
Creating an R script 22
Executing an R script 23
Vectors 24
Lists 26
Creating lists 26
Subsetting lists 27
Data frames 27
Functions 29
R's weaknesses and how to overcome them 31
Learning R effectively and minimizing the effort 33
The tidyverse 34
Leveraging the R community to learn R 34
Where to find the R community 35
Engaging with the community to learn R 35
Handling large datasets with R 37
Further references 38
Table of Contents
Summary 38
Chapter 2: A First Primer on Data Mining Analysing Your Bank Account
Data 39
Acquiring and preparing your banking data 40
Data model 40
Summarizing your data with pivot-like tables 41
A gentle introduction to the pipe operator 43
An even more gentle introduction to the dplyr package 45
Installing the necessary packages and loading your data into R 45
Installing and loading the necessary packages 46
Importing your data into R 46
Defining the monthly and daily sum of expenses 47
Visualizing your data with ggplot2 51
Basic data visualization principles 51
Less but better 52
Not every chart is good for your message 54
Scatter plot 54
Line chart 55
Bar plot 55
Other advanced charts 56
Colors have to be chosen carefully 57
A bit of theory - chromatic circle, hue, and luminosity 57
Visualizing your data with ggplot 60
One more gentle introduction – the grammar of graphics 61
A layered grammar of graphics – ggplot2 61
Visualizing your banking movements with ggplot2 62
Visualizing the number of movements per day of the week 62
Further references 66
Summary 66
Chapter 3: The Data Mining Process - CRISP-DM Methodology 68
The Crisp-DM methodology data mining cycle 69
Business understanding 71
Data understanding 71
Data collection 71
How to perform data collection with R 72
Data import from TXT and CSV files 72
Data import from different types of format already structured as tables 72
Data import from unstructured sources 72
Data description 73
How to perform data description with R 73
Data exploration 73
What to use in R to perform this task 74
[ ii ]
Table of Contents
[ iii ]
Table of Contents
Clarity 102
Clarity and mystery 103
Clarity and simplicity 103
Efficiency 103
Consistency 104
Syntax highlight 105
Auto-completion 106
How to build a data mining architecture in R 107
Data sources 107
The data warehouse 108
The data mining engine 108
The interface between the engine and the data warehouse 109
The data mining algorithms 109
The user interface 109
Further references 110
Summary 111
Chapter 5: How to Address a Data Mining Problem – Data Cleaning and
Validation 112
On a quiet day 113
Data cleaning 115
Tidy data 115
Analysing the structure of our data 117
The str function 117
The describe function 118
head, tail, and View functions 119
Evaluating your data tidiness 121
Every row is a record 121
Every column shows an attribute 122
Every table represents an observational unit 123
Tidying our data 124
The tidyr package 124
Long versus wide data 124
The spread function 127
The gather function 128
The separate function 129
Applying tidyr to our dataset 130
Validating our data 132
Fitness for use 132
Conformance to standards 133
Data quality controls 133
Consistency checks 134
Data type checks 134
Logical checks 134
Domain checks 135
[ iv ]
Table of Contents
[v]
Table of Contents
[ vi ]
Table of Contents
Summary 236
Chapter 9: Don't Give up – Power up Your Regression Including
Multiple Variables 238
Moving from simple to multiple linear regression 239
Notation 239
Assumptions 239
Variables' collinearity 240
Tolerance 241
Variance inflation factors 243
Addressing collinearity 243
Dimensionality reduction 243
Stepwise regression 244
Backward stepwise regression 245
From the full model to the n-1 model 246
Forward stepwise regression 248
Double direction stepwise regression 248
Principal component regression 249
Fitting a multiple linear model with R 251
Model fitting 251
Variable assumptions validation 254
Residual assumptions validation 256
Dimensionality reduction 257
Principal component regression 257
Stepwise regression 260
Linear model cheat sheet 265
Further references 266
Summary 266
Chapter 10: A Different Outlook to Problems with Classification Models 267
What is classification and why do we need it? 268
Linear regression limitations for categorical variables 268
Common classification algorithms and models 270
Logistic regression 272
The intuition behind logistic regression 272
The logistic function estimates a response variable enclosed within an upper and
lower bound 273
The logistic function estimates the probability of an observation pertaining to one of
the two available categories 274
The math behind logistic regression 274
Maximum likelihood estimator 276
Model assumptions 277
Absence of multicollinearity between variables 277
Linear relationship between explanatory variables and log odds 278
[ vii ]
Table of Contents
[ viii ]
Table of Contents
[ ix ]
Table of Contents
[x]
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Preface
You have probably heard that R is a fabulous tool that is gaining in popularity everyday
among data analysts and data scientists, and that it is renowned for its ability to deliver
highly flexible and professional results, paired with astonishing data visualizations. All this
sounds great, but how can you learn to use R as a data mining tool? This book will guide
you from the very beginning of this journey; you will not need to bring anything with you
except your curiosity, since we will discover everything we need along the way.
The book will help you develop these powerful skills through immersion in a crime case
that requires the use of data mining skills to solve, where you will be asked to help resolve a
real fraud case affecting a commercial company using both basic and advanced data mining
techniques.
At the end of our trip into the R world, you will be able to identify data mining problems,
analyze them, and correctly address them with the main data mining techniques (and some
advanced ones), producing astonishing final reports to convey messages and narrate the
stories you found within your data.
Chapter 2, A First Primer on Data Mining -Analyzing Your Bank Account Data, applies R to
our data.
Chapter 3, The Data Mining Process - the CRISP-DM Methodology, teaches you to organize
and conduct a data mining project through the CRISP-DM methodology.
Chapter 4, Keeping the Home Clean – The Data Mining Architecture, defines the static part of
our data mining projects, the data mining architecture.
Chapter 5, How to Address a Data Mining Problem – Data Cleaning and Validation, covers data
quality and data validation, where you will find out which metrics define the level of
quality of our data and discover a set of checks that can be employed to assess this quality.
Preface
Chapter 6, Looking into Your Data Eyes – Exploratory Data Analysis, teaches you about the
concept of exploratory data analysis and how it can be included within the data analysis
process.
Chapter 7, Our First Guess – A Linear Regression, lets us estimate a simple linear regression
model and check whether its assumptions have been satisfied.
Chapter 8, A Gentle Introduction to Model Performance Evaluation, covers the tools used to
define and measure the performance of data mining models.
Chapter 9, Don't Give Up – Power Up Your Regression Including Multiple Variables, predicts
the output of our response variable when more than one exploratory variable is involved.
Chapter 10, A Different Outlook to Problems with Classification Models, looks into classification
models, the need of them and they are uses.
Chapter 11, The Final Clash – Random Forest and Ensemble Learning, in this chapter we will
learn how to apply ensemble learning to estimated classification models.
Chapter 12, Looking for the Culprit – Text Data Mining with R, shows how to prepare the data
frame for text mining activities, removing irrelevant words and transforming it from a list
of sentences to a list of words. You also learn to perform sentiment analyses, wordcloud
development, and n-gram analyses on it.
Chapter 13, Sharing Your Stories with Your Stakeholders through R Markdown, employs R
markdown and shiny, two powerful instruments made available within the RStudio
ecosystem.
Chapter 14, Epilogue, is the unique background story made to learn the topics in a very
engaging manner.
Appendix, Dealing with Dates, Relative Paths, and Functions, includes additional information
to get things running in R.
[2]
Preface
Conventions
In this book, you will find a number of text styles that distinguish between different kinds
of information. Here are some examples of these styles and an explanation of their meaning.
Code words in text, database table names, folder names, filenames, file extensions, path
names, dummy URLs, user input, and Twitter handles are shown as follows: "Finally,
ggplot2 gives you the ability to highly customize your plot, adding every kind of graphical
or textual annotation to it."
Words that you see on the screen, for example, in menus or dialog boxes, appear in the text
like this: "In order to download new modules, we will go to Files | Settings | Project Name
| Project Interpreter."
[3]
Preface
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of a revolver, and the fourth provided himself with some cartridges
ready for contingencies. After the completion of these preparations, no
one either moved or spoke. The bear meanwhile, moved steadily
towards us, stopping for a moment at the spot where a piece of bread
had intentionally been placed. Just as he stopped to examine it, three
shots in rapid succession went off, and the bear, hit in the head and
chest, lay dead on the ground. The dogs, being let loose, rushed on
their fallen foe and began to tear his shaggy skin. While we were cutting
the bear up, they sat down and watched us, occasionally dipping their
tongues in the warm red blood and snapping up the morsels which were
thrown to them. The bear we had shot was a female, six feet in length;
and after cutting off the tongue and the best portions for meat, we
continued our march in the teeth of the driving snow. One of our people
had cut his finger badly in dressing the bear, and as the application of
chloride of iron did not suffice to stop the violent bleeding, we were
compelled to halt and erect our tent about six o’clock in the evening.
8. When we set out again on the morning of the 12th (the
thermometer marking -26° F.) all round us was a red undulating waste,
and the driving gusts of snow, which hid from our view the nearest
rocky heights, pricked us as if with countless sharp-pointed darts. Such
drifting snow, although it greatly impedes travelling, cannot be
compared with the tremendous snow-storms I had experienced in
Greenland. The same precursory signs were, however, common to both
—extraordinary refractions, brilliant auroras, perfect calms, and a dull
close atmosphere. In taking down the tent, which was covered with
wreaths of snow, every article which fell in it was at once buried under
its drifting waves. Of all the tests of endurance in Arctic journeys none
exceeds that of continuing the march amid driving snow at a low
temperature. Some of my company who had not been accustomed to
walk in such tremendous weather, in attempting to button on their wind-
screens and nose-bands and fasten up their coats after we had left the
tent, at once had their fingers frozen. Our sail-cloth boots were as hard
as stone, and every one took to stamping to preserve his feet from
frost-bite. Under such circumstances the sledge is not packed with that
precision which is the only preservative against the loss of the various
articles of its contents. To watch against this contingency is the special
business of the man who pushes the sledge from behind. Hurry and
confusion were visible in the bag of provisions being left open. At last
everything was ready: the march began, men and dogs, dragging the
sledge along, all coated with snow and entirely covered except the eyes.
In a momentary lull of the wind, we discovered that our march the day
before had led us far too much to the south, and Cape Tegetthoff now
lay before us directly north. Thither we now directed our steps, and as
the wind still came from the north-west, we struck our sledge sail. As a
consequence of this marching against the wind, which is most severely
felt by the leaders of the team, all, even Klotz, had their noses frost-
bitten. We had much difficulty in persuading him to rub his with snow,
urging that his nose did not belong to himself alone, but that seven
noses and fourteen feet were under the general supervision of the
leader, and that each had a share in this general property.
9. As we came under the land, the violence of the snow-drifting
somewhat abated, and in about two hours a calm set in. Close before us
lay the plateau of Cape Tegetthoff, with its steep precipitous sides. From
its summit a line of basalt rocks descended towards the east, ending in
two columns, each about two hundred feet high. We reached them just
before noon, and the weather being propitious we determined the
latitude by observation and found it to be 80° 6′ N.L. The force of the
tide not being able to raise or burst the bay-ice, the thaw-water of the
spring collects itself on the coast-edge in small lakes. Close under one of
these towers of dark-coloured basalt, we set up our tent; and while our
cook was preparing our dinner of bear’s flesh we lay in the sun under
the rocks in order to dry our clothes, which were coated all over with
ice.
CAPE TEGETTHOFF.
10. About one o’clock I set off with the Tyrolese to the plateau of
Cape Tegetthoff. Those who remained behind spent their time in rubbing
their feet with snow. Lettis had reserved for us the unpleasant surprise
that his feet had been frost-bitten for three hours, and that he had lost
all feeling in them. We marched for an hour on the snow, which lay in
tender azure-blue shadow under the long line of basalt rocks, and after
climbing for another hour over rosy-coloured masses of snow lying
between crystallized rocks, we reached the highest point of the
undulating plateau. No ascent could be more interesting, made, as it
was, in a country so utterly unknown. Haller and Klotz were born
mountaineers, and during my surveys in Tyrol I had made a hundred
ascents of mountains of 10,000 feet, without the tension of expectation
I now experienced, as I mounted this summit. The ascent was not
without difficulty, and it taxed the extraordinary dexterity of the two
Tyrolese to climb up steep icy precipices in their sail-cloth boots. It was
about three o’clock in the afternoon when we reached the summit; the
temperature had fallen to -30° F. (in the tent the thermometer at the
same time marked -24° F. and in the ship -20° F.). By a barometrical
measurement we found the height to be 2,600 feet. Contrary to
expectation the view from the top proved to be limited. In a northerly
direction, the atmosphere, laden with innumerable ice crystals,
possessed so little transparency that Cape Berghaus, at no distance off,
appeared to be covered with a thick veil, and all distant objects were
enveloped in a dense mist. Fogs lay over the interior to the west, and
banks of reddish vapour covered the icy ocean to the south. Some
narrow strips of open water sparkled in the sun. After making a sketch
of all that could be distinctly seen, and determining the bearings of
some points, we returned to the tent. Here we found Lettis and
Cattarinch engaged in rubbing with snow the hands of Lukinovich, which
had been frost-bitten, while he was occupied in rubbing the feet of
Lettis.
11. Nothing except the wind makes men so sensitive to cold as the
want of exercise. The fall of the temperature had been felt far more by
those who remained behind, than by ourselves. Even the wonderful
beauty of the snow-clad summit bathed in rosy light failed to modify
their severe judgment of Franz-Josef Land. Instead of greeting us with
supper ready at the appointed hour, which he ought to have prepared
without the use of spirit, the bewildered cook was vainly endeavouring
to roast bear’s flesh over smoky chips and sticks, and we got our supper
only after I had served out a bottle of alcohol. We then went to rest in
the common sleeping bag, but soon began to shake with cold, which
threw Pospischill, who took oil twice a day for lung-disease, into a fever.
When I left the tent to look at the thermometers, the mercury in one
had gone down into the bulb and was frozen, and the spirits of wine in
the other showed 41° below zero (C.). Some hot grog, for which a
whole bottle of strong rum was used, put us all right, raising the
temperature of our bodies by one or two degrees. After this refreshment
we all fell into a deep sleep, which was incommoded only by the
increasing dampness of our clothes.
12. We started again about six o’clock on the morning of March 13.
The sun had not risen, the spirit of wine thermometer indicated nearly
44° (C.) below zero, and a piercingly cold breeze met us from the land.
Even on board the ship the temperature at the same time marked 37°
(C.) below zero, a difference to be ascribed to the influence of the land
in lowering the temperature. In Greenland we observed still greater
deviations of this nature, which seem to show that climatical influences
are subject to great variations, even in places which are in close
proximity. Cape Berghaus was our goal. From its summit a general view
of the distribution of the land under 80° N. lat. was reasonably to be
expected. Long before the rise of the sun, the hard snowy plains were
tinted with a pale green reflected light, and the icebergs wore a dull
silvery hue, while their outlines constantly changed and undulated. Our
road was formed from millions of glittering snow crystals, so hard that
the sledge glided over them with difficulty and with a creaking noise,
and after three hours, the exertion of dragging had so exhausted us that
we determined to unload the sledge, and, after melting some snow, to
wet its runners with water. A layer of ice was immediately formed on
them, which greatly facilitated the labour of dragging, till it was rubbed
off. A broad inlet surrounded by picturesque mountains—Nordenskjöld
Fiord—had opened out on our left, and as a large glacier formed the
background of this fiord, we took a westerly direction in order to study
the ice-formation. The heights surrounding this fiord seemed equally as
well fitted as Cape Berghaus for the object we had in view. The further
we penetrated into it, the deeper became the layer of fine powdery
snow which the wind had deposited in this hollow. At noon we reached
the high precipitous termination of Sonklar-Glacier, and pitched our tent
by an iceberg.
CHAPTER V.
THE COLD.
1. THE coldest day we had during this expedition was the 14th of
March. By six o’clock on the morning of that day the Tyrolese and I
stood on the summit of the precipitous face of the Sonklar-Glacier. The
others remained behind to clear the tent of snow, and to bury a small
depôt of provisions in an iceberg which was close at hand. The sun had
not yet risen, though a golden gleam behind the glaciers of Salm Island
indicated his near approach. At last the sun himself appeared, blood-
red, glowing with indistinct outline through the mists, and surrounded
with parhelia, which generally occur when the cold is great. The tops of
the high snowy mountains were first touched with rosy light, which
gradually descended and spread over the icy plains, and the sun like a
ball of fire shone at length clearly through the frosty mist, and
everything around seemed on fire. As the sun even at noon was but a
few degrees above the horizon, this wonderful colouring lasted
throughout the day, and the mountains, whose steepest sides were
covered with a frosty efflorescence, shone like glass in this radiant light.
The alcohol thermometer soon after we came on the glacier fell to 59°
1′ (F.) below zero,[34] and a light breeze blowing from the interior, which
would have been pleasant enough on a March day in Europe, exposed
me, while engaged in the indispensable work of drawing and measuring,
to such danger, that though I worked under the shelter of my Tyrolese
companions as a protection against the cold, I was constantly compelled
to rub my stiffened and benumbed hands with snow. We had taken
some rum with us, and as each took his share, he knelt down and
allowed another to shake it into his mouth, without bringing the metal
cup in contact with his lips. This rum, though it was strong, seemed to
have lost all its strength and fluidity. It tasted like innocent milk, and its
consistence was that of oil. The bread was frozen so hard that we
feared to break our teeth in biting it, and it brought blood as we ate it.
The attempt to smoke a cigar was a punishment rather than an
enjoyment, because the icicles on our beards always put them out, and
when we took them out of our mouths they were frozen. Even the
shortest pipes met the same fate. The instruments I used in surveying
seemed to burn when I touched them, and the medals which my
companions wore on their breasts felt like hot iron.
ON THE SONKLAR-GLACIER.
BLOCK OF SNOW.
12. We now slept without stirring a limb, and about five o’clock in the
morning of the 15th of March we started to compass the twenty miles
which lay between us and the ship in one march, without encountering
the suffering of another night’s camping out in the snow. The weather
was as clear as it is possible to be at a temperature of -52° F., and going
along with a light breeze from the north, we made use of our sledge sail
to such advantage that we reached the gentle ascent of the west point
of Wilczek Island after a march of seven hours. We formed a second
depôt of provisions on the summit of a rocky promontory, whence we
discerned with a telescope the masts and yards of the ship lying behind
an iceberg, and our fears and anxieties lest it should have drifted away
in our absence were dissipated by this glad view. Our return to the ship
could no longer be a matter of choice; it had become a necessity. Lettis
had been unable for some days to take any share in the labour of
dragging, and walked along in shoes made of reindeer hide, on account
of his frost-bitten feet. Haller also wore similar shoes to save his swollen
feet; Cattarinch’s face was frost-bitten, and he too suffered from
lameness; Pospischill, who could no longer wear his shrunk-up fur coat,
so suffered from frost-bite in both hands, that I sent him on to the ship,
that he might have the help of the doctor as soon as possible. It was
with much effort that we made the last six hours’ march; and when at
length, stiff with ice, we passed between the hummocks that lay around
the ship, Weyprecht, Brosch, Orel, and eight sailors came to meet us,
who, alarmed at the inability of Pospischill to speak in answer to their
questions, had set out from the ship in order to find us.
CHAPTER VI.
A GENERAL DESCRIPTION OF KAISER FRANZ-JOSEF LAND.
HIPPOLYTE PAYERI.
HYALONEMA LONGISSIMUM.
KORETHRASTES HISPIDUS.
NEPHTHYS LONGISETOSA.
CHAPTER VII.
THE SECOND SLEDGE EXPEDITION.—AUSTRIA SOUND.