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Essential Statistics for Non-STEM Data Analysts

Copyright © 2020 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,
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Contributors
About the author
Rongpeng Li is a data science instructor and a senior data scientist at Galvanize, Inc. He
has previously been a research programmer at Information Sciences Institute, working on
knowledge graphs and artificial intelligence. He has also been the host and organizer of
the Data Analysis Workshop Designed for Non-STEM Busy Professionals at LA.

Michael Hansen (https://www.linkedin.com/in/michael-n-hansen/), a


friend of mine, provided invaluable English language editing suggestions
for this book. Michael has great attention to detail, which made him a great
language reviewer. Thank you, Michael!
About the reviewers
James Mott, PhD, is a senior education consultant with extensive experience in teaching
statistical analysis, modeling, data mining, and predictive analytics. He has over 30 years
of experience using SPSS products in his own research, including IBM SPSS Statistics,
IBM SPSS Modeler, and IBM SPSS Amos. He has also been actively teaching about these
products to IBM/SPSS customers for over 30 years. In addition, he is an experienced
historian with expertise in the research and teaching of 20th century United States
political history and quantitative methods. His specialties are data mining, quantitative
methods, statistical analysis, teaching, and consulting.

Yidan Pan obtained her PhD in system, synthetic, and physical biology from Rice
University. Her research interest is profiling mutagenesis at genomic and transcriptional
levels with molecular biology wet labs, bioinformatics, statistical analysis, and machine
learning models. She believes that this book will give its readers a lot of practical skills for
data analysis.

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Table of Contents

Preface

Section 1: Getting Started with Statistics for


Data Science
1
Fundamentals of Data Collection, Cleaning, and
Preprocessing
Technical requirements 4 frequent value 18
Collecting data from various Outlier removal 20
data sources 5
Data standardization – when
Reading data directly from files  5
and how 21
Obtaining data from an API 6
Obtaining data from scratch 9
Examples involving the scikit-
learn preprocessing module 23
Data imputation 11 Imputation23
Preparing the dataset for imputation 11 Standardization23
Imputation with mean or median values 16
Summary24
Imputation with the mode/most

2
Essential Statistics for Data Assessment
Classifying numerical and Understanding mean, median,
categorical variables 26 and mode 30
Distinguishing between numerical and Mean30
categorical variables 26 Median31
Mode32
ii Table of Contents

Learning about variance, data types 43


standard deviation, quartiles, Frequencies and proportions 43
percentiles, and skewness 33 Transforming a continuous variable to
Variance33 a categorical one 46
Standard deviation 36
Using bivariate and
Quartiles37
multivariate descriptive statistics47
Skewness39
Covariance48
Knowing how to handle Cross-tabulation50
categorical variables and mixed
Summary51

3
Visualization with Statistical Graphs
Basic examples with the plotting72
Python Matplotlib package 54 Example 1 – preparing data to fit the
Elements of a statistical graph 54 plotting
Exploring important types of plotting function API 73
in Matplotlib 56 Example 2 – combining analysis with
plain plotting 76
Advanced visualization
customization65 Presentation-ready plotting tips 78
Customizing the geometry 65 Use styling 78
Customizing the aesthetics 70 Font matters a lot 80

Query-oriented statistical Summary80

Section 2: Essentials of Statistical Analysis


4
Sampling and Inferential Statistics
Understanding fundamental The dangers associated with non-
concepts in sampling techniques84 probability sampling 86
Performing proper sampling Probability sampling – the safer
approach88
under
different scenarios 86 Understanding statistics
associated with sampling 98
Table of Contents iii

Sampling distribution of the The central limit theorem 107


sample mean 98
Standard error of the sample mean 103 Summary108

5
Common Probability Distributions
Understanding important distribution  121
concepts in probability 110 Uniform distribution 122
Events and sample space 110 Exponential distribution 122
The probability mass function and Normal distribution 124
the probability density function 111
Subjective probability and Learning about joint and
empirical probability 116 conditional distribution 126
Independency and conditional
Understanding common distribution127
discrete probability
distributions116 Understanding the power law
Bernoulli distribution 117 and black swan 127
Binomial distribution 118 The ubiquitous power law 128
Poisson distribution 120 Be aware of the black swan 129

Understanding the common Summary130


continuous probability

6
Parametric Estimation
Understanding the concepts of Applying the maximum
parameter estimation and the likelihood approach with
features of estimators 132 Python141
Evaluation of estimators 133 Likelihood function 141
MLE for uniform distribution
Using the method of moments boundaries144
to estimate parameters 136 MLE for modeling noise 145
Example 1 – the number of 911 phone MLE and the Bayesian theorem 155
calls in a day 137
Example 2 – the bounds of Summary160
uniform distribution 139
iv Table of Contents

7
Statistical Hypothesis Testing
An overview of hypothesis The paradigm  180
testing162 T-test181
Understanding P-values, test statistics, The normality hypothesis test 185
and significance levels 164 The goodness-of-fit test 189
A simple ANOVA model 192
Making sense of confidence Stationarity tests for time series 197
intervals and P-values from Examples of stationary and non-
visual examples 167 stationary time series 198
Calculating the P-value from discrete
events168 Appreciating A/B testing with a
Calculating the P-value from the real-world example 206
continuous PDF 170 Conducting an A/B test 206
Significance levels in t-distribution 174 Randomization and blocking 207
The power of a hypothesis test 179 Common test statistics 210
Common mistakes in A/B tests 211
Using SciPy for common
hypothesis testing  180 Summary212

Section 3: Statistics for Machine Learning


8
Statistics for Regression
Understanding a simple Simple linear regression as an
linear regression model and estimator232
its rich content 216
Having hands-on experience
Least squared error linear regression
with multivariate linear
and variance decomposition 220
regression and collinearity
The coefficient of determination 227
analysis233
Hypothesis testing 230
Collinearity239
Connecting the relationship
Learning regularization from
between regression and
logistic regression examples 241
estimators230
Summary246
Table of Contents v

9
Statistics for Classification
Understanding how a logistic Evaluating the performance of the
regression classifier works 248 logistic regression classifier 256
The formulation of a
Building a naïve Bayes classifier
classification problem 250
from scratch 259
Implementing logistic regression
from scratch 251 Underfitting, overfitting, and
cross-validation267
Summary272

10
Statistics for Tree-Based Methods
Overviewing tree-based Evaluating decision tree performance 287
methods for classification tasks274
Exploring regression tree 289
Growing and pruning a
classification tree 278 Using tree models in scikit-learn296
Understanding how splitting works 279 Summary298

11
Statistics for Ensemble Methods
Revisiting bias, variance, and Understanding and using the
memorization300 boosting module 311
Understanding the Exploring random forests with
bootstrapping and bagging scikit-learn316
techniques303 Summary  318
vi Table of Contents

Section 4: Appendix
12
A Collection of Best Practices
Understanding the importance Example 1 – COVID-19 trend 326
of data quality 322 Example 2 – Bar plot cropping 328
Understanding why data can be Fighting against false arguments 334
problematic322
Summary335
Avoiding the use of misleading
graphs326

13
Exercises and Projects
Exercises338 Methods351
Chapter 1 – Fundamentals of Data Chapter 11 – Statistics for Ensemble
Collection, Cleaning, and Preprocessing 338 Methods353
Chapter 2 – Essential Statistics for Data
Project suggestions 355
Assessment339
Chapter 3 – Visualization with Non-tabular data 355
Statistical Graphs 340 Real-time weather data 356
Chapter 4 – Sampling and Inferential Goodness of fit for discrete
Statistics341 distributions358
Chapter 5 – Common Probability Building a weather prediction web app 359
Distributions342 Building a typing suggestion app 360
Chapter 6 – Parameter Estimation 344
Chapter 7 – Statistical Hypothesis Further reading 360
Testing346 Textbooks361
Chapter 8 – Statistics for Regression 348 Visualization361
Chapter 9 – Statistics for Classification 349 Exercising your mind 361
Chapter 10 – Statistics for Tree-Based
Summary362
Other Books You May Enjoy
Index
Preface
Data science has been trending for several years, and demand in the market is now really
on the increase as companies, governments, and non-profit organizations have shifted
toward a data-driven approach.
Many new graduates, as well as people who have been working for years, are now trying
to add data science as a new skill to their resumes. One significant barrier for stepping
into the realm of data science is statistics, especially for people who do not have a science,
technology, engineering, and mathematics (STEM) background or left the classroom
years ago. This book is designed to fill the gap for those people. While writing this book,
I tried to explore the scattered concepts in a dot-connecting fashion such that readers
feel that new concepts and techniques are needed rather than simply being created from
thin air.
By the end of this book, you will be able to comfortably deal with common statistical
concepts and computation in data science, from fundamental descriptive statistics and
inferential statistics to advanced topics, such as statistics using tree-based methods and
ensemble methods. This book is also particularly handy if you are preparing for a data
scientist or data analyst job interview. The nice interleaving of conceptual contents and
code examples will prepare you well.

Who this book is for


This book is for people who are looking for materials to fill the gaps in their statistics
knowledge. It should also serve experienced data scientists as an enjoyable read. The book
assumes minimal mathematics knowledge and it may appear verbose, as it is designed so
that novices can use it as a self-contained book and follow the book chapter by chapter
smoothly to build a knowledge base on statistics from the ground up.
viii Preface

What this book covers


Chapter 1, Fundamentals of Data Collection, Cleaning, and Preprocessing, introduces basic
concepts in data collection, cleaning, and simple preprocessing.
Chapter 2, Essential Statistics for Data Assessment, talks about descriptive statistics, which
are handy for the assessment of data quality and exploratory data analysis (EDA).
Chapter 3, Visualization with Statistical Graphs, introduces common graphs that suit
different visualization scenarios.
Chapter 4, Sampling and Inferential Statistics, introduces the fundamental concepts and
methodologies in sampling and the inference techniques associated with it.
Chapter 5, Common Probability Distributions, goes through the most common discrete
and continuous distributions, which are the building blocks for more sophisticated real-
life empirical distributions.
Chapter 6, Parametric Estimation, covers a classic and rich topic that solidifies your
knowledge of statistics and probability by having you estimate parameters from
accessible datasets.
Chapter 7, Statistical Hypothesis Testing, looks at a must-have skill for any data scientist
or data analyst. We will cover the full life cycle of hypothesis testing, from assumptions to
interpretation.
Chapter 8, Statistics for Regression, discusses statistics for regression problems, starting
with simple linear regression.
Chapter 9, Statistics for Classification, explores statistics for classification problems,
starting with logistic regression.
Chapter 10, Statistics for Tree-Based Methods, delves into statistics for tree-based methods,
with a detailed walk through of building a decision tree from first principles.
Chapter 11, Statistics for Ensemble Methods, moves on to ensemble methods, which are
meta-algorithms built on top of basic machine learning or statistical algorithms. This
chapter is dedicated to methods such as bagging and boosting.
Chapter 12, Best Practice Collection, introduces several important practice tips based on
the author's data science mentoring and practicing experience.
Chapter 13, Exercises and Projects, includes exercises and project suggestions grouped
by chapter.
Preface ix

To get the most out of this book


As Jupyter notebooks can run on Google Colab, a computer connected to the internet and
a Google account should be sufficient.

If you are using the digital version of this book, we advise you to type the code yourself
or access the code via the GitHub repository (link available in the next section). Doing
so will help you avoid any potential errors related to the copying and pasting of code.

Download the example code files


You can download the example code files for this book from GitHub at https://
github.com/PacktPublishing/Essential-Statistics-for-Non-STEM-
Data-Analysts. In case there's an update to the code, it will be updated on the existing
GitHub repository.
We also have other code bundles from our rich catalog of books and videos available at
https://github.com/PacktPublishing/. Check them out!

Download the color images


We also provide a PDF file that has color images of the screenshots/diagrams used
in this book. You can download it here: https://static.packt-cdn.com/
downloads/9781838984847_ColorImages.pdf.

Conventions used
There are a number of text conventions used throughout this book.
Code in text: Indicates code words in text, database table names, folder names,
filenames, file extensions, pathnames, dummy URLs, user input, and Twitter handles.
Here is an example: " You can use plt.rc('ytick', labelsize='x-
medium')."
x Preface

A block of code is set as follows:

import pandas as pd

df = pd.read_excel("PopulationEstimates.xls",skiprows=2)

df.head(8) margin: 0;

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

$ pip install pandas

Bold: Indicates a new term, an important word, or words that you see onscreen. For
example, words in menus or dialog boxes appear in the text like this. Here is an example: "
seaborn is another popular Python visualization library. With it, you can write less code to
obtain more professional-looking plots."

Tips or important notes


R is another famous programming language for data science and statistical
analysis. There are also successful R packages. The counterpart of Matplotlib is
the R ggplot2 package I mentioned above.

Get in touch
Feedback from our readers is always welcome.
General feedback: If you have questions about any aspect of this book, mention the book
title in the subject of your message and email us at [email protected].
Errata: Although we have taken every care to ensure the accuracy of our content, mistakes
do happen. If you have found a mistake in this book, we would be grateful if you would
report this to us. Please visit www.packtpub.com/support/errata, selecting your
book, clicking on the Errata Submission Form link, and entering the details.
Piracy: If you come across any illegal copies of our works in any form on the Internet,
we would be grateful if you would provide us with the location address or website name.
Please contact us at [email protected] with a link to the material.
If you are interested in becoming an author: If there is a topic that you have expertise in
and you are interested in either writing or contributing to a book, please visit authors.
packtpub.com.
Preface xi

Reviews
Please leave a review. Once you have read and used this book, why not leave a review on
the site that you purchased it from? Potential readers can then see and use your unbiased
opinion to make purchase decisions, we at Packt can understand what you think about
our products, and our authors can see your feedback on their book. Thank you!
For more information about Packt, please visit packt.com.
Section 1:
Getting Started
with Statistics for
Data Science

In this section, you will learn how to preprocess data and inspect distributions and
correlations from a statistical perspective.
This section consists of the following chapters:

• Chapter 1, Fundamentals of Data Collection, Cleaning, and Preprocessing


• Chapter 2, Essential Statistics for Data Assessment
• Chapter 3, Visualization with Statistical Graphs
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