Practical Data Analysis - Second Edition

Table of Contents

Practical Data Analysis - Second Edition

Credits

About the Authors

About the Reviewers

www.PacktPub.com

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Why subscribe?

Free access for Packt account holders

Preface

What this book covers

What you need for this book

Who this book is for

Conventions

Reader feedback

Customer support

Downloading the example code

Downloading the color images of this book

Errata

Piracy

Questions

1. Getting Started

Computer science

Artificial intelligence

Machine learning

Statistics

Mathematics

Knowledge domain

Data, information, and knowledge

Inter-relationship between data, information, and knowledge

The nature of data

The data analysis process

The problem

Data preparation

Data exploration

Predictive modeling

Visualization of results

Quantitative versus qualitative data analysis

Importance of data visualization

What about big data?

Quantified self

Sensors and cameras

Social network analysis

Tools and toys for this book

Why Python?

Why mlpy?

Why D3.js?

Why MongoDB?

Summary

2. Preprocessing Data

Data sources

Open data

Text files

Excel files

SQL databases

NoSQL databases

Multimedia

Web scraping

Data scrubbing

Statistical methods

Text parsing

Data transformation

Data formats

Parsing a CSV file with the CSV module

Parsing CSV file using NumPy

JSON

Parsing JSON file using the JSON module

XML

Parsing XML in Python using the XML module

YAML

Data reduction methods

Filtering and sampling

Binned algorithm

Dimensionality reduction

Getting started with OpenRefine

Text facet

Clustering

Text filters

Numeric facets

Transforming data

Exporting data

Operation history

Summary

3. Getting to Grips with Visualization

What is visualization?

Working with web-based visualization

Exploring scientific visualization

Visualization in art

The visualization life cycle

Visualizing different types of data

HTML

DOM

CSS

JavaScript

SVG

Getting started with D3.js

Bar chart

Pie chart

Scatter plots

Single line chart

Multiple line chart

Interaction and animation

Data from social networks

An overview of visual analytics

Summary

4. Text Classification

Learning and classification

Bayesian classification

Naïve Bayes

E-mail subject line tester

The data

The algorithm

Classifier accuracy

Summary

5. Similarity-Based Image Retrieval

Image similarity search

Dynamic time warping

Processing the image dataset

Implementing DTW

Analyzing the results

Summary

6. Simulation of Stock Prices

Financial time series

Random Walk simulation

Monte Carlo methods

Generating random numbers

Implementation in D3js

Quantitative analyst

Summary

7. Predicting Gold Prices

Working with time series data

Components of a time series

Smoothing time series

Lineal regression

The data - historical gold prices

Nonlinear regressions

Kernel Ridge Regressions

Smoothing the gold prices time series

Predicting in the smoothed time series

Contrasting the predicted value

Summary

8. Working with Support Vector Machines

Understanding the multivariate dataset

Dimensionality reduction

Linear Discriminant Analysis (LDA)

Principal Component Analysis (PCA)

Getting started with SVM

Kernel functions

The double spiral problem

SVM implemented on mlpy

Summary

9. Modeling Infectious Diseases with Cellular Automata

Introduction to epidemiology

The epidemiology triangle

The epidemic models

The SIR model

Solving the ordinary differential equation for the SIR model with SciPy

The SIRS model

Modeling with Cellular Automaton

Cell, state, grid, neighborhood

Global stochastic contact model

Simulation of the SIRS model in CA with D3.js

Summary

10. Working with Social Graphs

Structure of a graph

Undirected graph

Directed graph

Social networks analysis

Acquiring the Facebook graph

Working with graphs using Gephi

Statistical analysis

Male to female ratio

Degree distribution

Histogram of a graph

Centrality

Transforming GDF to JSON

Graph visualization with D3.js

Summary

11. Working with Twitter Data

The anatomy of Twitter data

Tweet

Followers

Trending topics

Using OAuth to access Twitter API

Getting started with Twython

Simple search using Twython

Working with timelines

Working with followers

Working with places and trends

Working with user data

Streaming API

Summary

12. Data Processing and Aggregation with MongoDB

Getting started with MongoDB

Database

Collection

Document

Mongo shell

Insert/Update/Delete

Queries

Data preparation

Data transformation with OpenRefine

Inserting documents with PyMongo

Group

Aggregation framework

Pipelines

Expressions

Summary

13. Working with MapReduce

An overview of MapReduce

Programming model

Using MapReduce with MongoDB

Map function

Reduce function

Using mongo shell

Using Jupyter

Using PyMongo

Filtering the input collection

Grouping and aggregation

Counting the most common words in tweets

Summary

14. Online Data Analysis with Jupyter and Wakari

Getting started with Wakari

Creating an account in Wakari

Getting started with IPython notebook

Data visualization

Introduction to image processing with PIL

Opening an image

Working with an image histogram

Filtering

Operations

Transformations

Getting started with pandas

Working with Time Series

Working with multivariate datasets with DataFrame

Grouping, Aggregation, and Correlation

Sharing your Notebook

The data

Summary

15. Understanding Data Processing using Apache Spark

Platform for data processing

The Cloudera platform

Installing Cloudera VM

An introduction to the distributed file system

First steps with Hadoop Distributed File System - HDFS

File management with HUE - web interface

An introduction to Apache Spark

The Spark ecosystem

The Spark programming model

An introductory working example of Apache Startup

Summary

Practical Data Analysis - Second Edition

Practical Data Analysis - Second Edition

Copyright © 2016 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 authors, 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.

First published: October 2013

Second published: September 2016

Production reference: 1260916

Published by Packt Publishing Ltd.

Livery Place

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Birmingham B3 2PB, UK.

ISBN 978-1-78528-971-2

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Credits

About the Authors

Hector Cuesta is founder and Chief Data Scientist at Dataxios, a machine intelligence research company. Holds a BA in Informatics and a M.Sc. in Computer Science. He provides consulting services for data-driven product design with experience in a variety of industries including financial services, retail, fintech, e-learning and Human Resources. He is an enthusiast of Robotics in his spare time.

You can follow him on Twitter at https://twitter.com/hmCuesta.

I would like to dedicate this book to my wife Yolanda, and to my wonderful children Damian and Isaac for all the joy they bring into my life. To my parents Elena and Miguel for their constant support and love. 

Dr. Sampath Kumar works as an assistant professor and head of Department of Applied Statistics at Telangana University. He has completed M.Sc., M.Phl., and Ph. D. in statistics. He has five years of teaching experience for PG course. He has more than four years of experience in the corporate sector. His expertise is in statistical data analysis using SPSS, SAS, R, Minitab, MATLAB, and so on. He is an advanced programmer in SAS and matlab software. He has teaching experience in different, applied and pure statistics subjects such as forecasting models, applied regression analysis, multivariate data analysis, operations research, and so on for M.Sc. students. He is currently supervising Ph.D. scholars.

About the Reviewers

Chandana N.  Athauda is currently employed at BAG (Brunei Accenture Group) Networks—Brunei and he serves as a technical consultant. He mainly focuses on Business Intelligence, Big Data and Data Visualization tools and technologies.

He has been working professionally in the IT industry for more than 15 years (Ex-Microsoft Most Valuable Professional (MVP) and Microsoft Ranger for TFS). His roles in the IT industry have spanned   the entire spectrum from programmer to technical consultant. Technology has always been a passion for him.

If you would like to talk to Chandana about this book, feel free to write to him at info @inzeek.net or by giving him a tweet @inzeek.

Mark Kerzner is a Big Data architect and trainer. Mark is a founder and principal at Elephant Scale, offering Big Data training and consulting. Mark has written HBase Design Patterns for Packt.

I would like to acknowledge my co-founder Sujee Maniyam and his colleague Tim Fox, as well as all the students and teachers. Last but not least, thanks to my multi-talented family.

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Preface

Practical Data Analysis provides a series of practical projects in order to turn data into insight. It covers a wide range of data analysis tools and algorithms for classification, clustering, visualization, simulation and forecasting. The goal of this book is to help you to understand your data to find patterns, trends, relationships and insight.

This book contains practical projects that take advantage of the MongoDB, D3.js, Python language and its ecosystem to present the concepts using code snippets and detailed descriptions.

What this book covers

Chapter 1, Getting Started, In this chapter, we discuss the principles of data analysis and the data analysis process.

Chapter 2, Preprocessing Data, explains how to scrub and prepare your data for the analysis, also introduces the use of OpenRefine which is a Data Cleansing tool.

Chapter 3, Getting to Grips with Visualization, shows how to visualize different kinds of data using D3.js which is a JavaScript Visualization Framework.

Chapter 4, Text Classification, introduces the binary classification using a Naïve Bayes Algorithm to classify spam.

Chapter 5, Similarity-Based Image Retrieval, presents a project to find the Similarity between images using a dynamic time warping approach.

Chapter 6, Simulation of Stock Prices, explains how to simulate a Stock Price using Random Walk algorithm, visualized with a D3.js animation.

Chapter 7, Predicting Gold Prices, introduces how Kernel Ridge Regression works, and how to use it to predict the gold price using time series.

Chapter 8, Working with Support Vector Machines, describes how to use Support Vector Machines as a classification method.

Chapter 9, Modeling Infectious Diseases with Cellular Automata, introduces the basic concepts of Computational Epidemiology simulation and explains how to implement a cellular automaton to simulate an epidemic outbreak using D3.js and JavaScript.

Chapter 10, Working with Social Graphs, explains how to obtain and visualize your social media graph from Facebook using Gephi.

Chapter 11, Working with Twitter Data, explains how to use the Twitter API to retrieve data from twitter. We also see how to improve the text classification to perform a sentiment analysis using the Naïve Bayes Algorithm implemented in the Natural Language Toolkit (NLTK).

Chapter 12, Data Processing and Aggregation with MongoDB, introduces the basic operations in MongoDB as well as methods for grouping, filtering, and aggregation.

Chapter 13, Working with MapReduce, illustrates how to use the MapReduce programming model implemented in MongoDB.

Chapter 14, Online Data Analysis with Jupyter and Wakari, explains how to use the Wakari platform and introduces the basic use of Pandas and PIL with IPython.

Chapter 15, Understanding Data Processing using Apache Spark, explains how to use distributed file system along with Cloudera VM and how to get started with a data environment. Finally, we describe the main features of Apache Spark with a practical example.

What you need for this book

The basic requirements for this book are as follows:

Python

OpenRefine

D3.js

Mlpy

Natural Language Toolkit (NLTK)

Gephi

MongoDB

Who this book is for

This book is for Software Developers, Analyst and Computer Scientists who want to implement data analysis and visualization in a practical way. The book is also intended to provide a self-contained set of practical projects in order to get insight from different kinds of data like, time series, numerical, multidimensional, social media graphs and texts.

You are not required to have previous knowledge about data analysis, but some basic knowledge about statistics and a general understanding of Python programming is assumed.

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, pathnames, dummy URLs, user input, and Twitter handles are shown as follows: For this example, we will use the BeautifulSoup library version 4.

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from bs4 import BeautifulSoup

import urllib.request

from time import sleep

from datetime import datetime

Any command-line input or output is written as follows:

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Note

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Tip

Tips and tricks appear like this.

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