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Computational and Inferential Thinking: The Foundations of Data

Science
Contents
1. Data Science
2. Causality and Experiments
3. Programming in Python
4. Data Types
5. Sequences
6. Tables
7. Visualization
8. Functions and Tables
9. Randomness
10. Sampling and Empirical Distributions
11. Testing Hypotheses
12. Comparing Two Samples
13. Estimation
14. Why the Mean Matters
15. Prediction
16. Inference for Regression
17. Classification
18. Updating Predictions
2nd Edition by Ani Adhikari, John DeNero, David Wagner.
This text was originally developed for the UC Berkeley course Data 8: Foundations of Data Science.
You can view this text online or view the source.
The contents of this book are licensed for free consumption under the following license: Creative Commons Attribution‑NonCommercial‑
NoDerivatives 4.0 International (CC BY‑NC‑ND 4.0).

1. What is Data Science?

Data Science is about drawing useful conclusions from large and diverse data sets through exploration, prediction, and inference. Exploration
involves identifying patterns in information. Prediction involves using information we know to make informed guesses about values we wish we knew.
Inference involves quantifying our degree of certainty: will the patterns that we found in our data also appear in new observations? How accurate are
our predictions? Our primary tools for exploration are visualizations and descriptive statistics, for prediction are machine learning and optimization,
and for inference are statistical tests and models.
Statistics is a central component of data science because statistics studies how to make robust conclusions based on incomplete information.
Computing is a central component because programming allows us to apply analysis techniques to the large and diverse data sets that arise in real‑
world applications: not just numbers, but text, images, videos, and sensor readings. Data science is all of these things, but it is more than the sum of
its parts because of the applications. Through understanding a particular domain, data scientists learn to ask appropriate questions about their data
and correctly interpret the answers provided by our inferential and computational tools.
1.1. Chapter 1: Introduction
Data are descriptions of the world around us, collected through observation and stored on computers. Computers enable us to infer properties of the
world from these descriptions. Data science is the discipline of drawing conclusions from data using computation. There are three core aspects of
effective data analysis: exploration, prediction, and inference. This text develops a consistent approach to all three, introducing statistical ideas and
fundamental ideas in computer science concurrently. We focus on a minimal set of core techniques that can be applied to a vast range of real‑world
applications. A foundation in data science requires not only understanding statistical and computational techniques, but also recognizing how they
apply to real scenarios.
For whatever aspect of the world we wish to study—whether it’s the Earth’s weather, the world’s markets, political polls, or the human mind—data we
collect typically offer an incomplete description of the subject at hand. A central challenge of data science is to make reliable conclusions using this
partial information.
In this endeavor, we will combine two essential tools: computation and randomization. For example, we may want to understand climate change
trends using temperature observations. Computers will allow us to use all available information to draw conclusions. Rather than focusing only on the
average temperature of a region, we will consider the whole range of temperatures together to construct a more nuanced analysis. Randomness will
allow us to consider the many different ways in which incomplete information might be completed. Rather than assuming that temperatures vary in a
particular way, we will learn to use randomness as a way to imagine many possible scenarios that are all consistent with the data we observe.
Applying this approach requires learning to program a computer, and so this text interleaves a complete introduction to programming that assumes
no prior knowledge. Readers with programming experience will find that we cover several topics in computation that do not appear in a typical
introductory computer science curriculum. Data science also requires careful reasoning about numerical quantities, but this text does not assume any
background in mathematics or statistics beyond basic algebra. You will find very few equations in this text. Instead, techniques are described to
readers in the same language in which they are described to the computers that execute them—a programming language.

1.1.1. Computational Tools

This text uses the Python 3 programming language, along with a standard set of numerical and data visualization tools that are used widely in
commercial applications, scientific experiments, and open‑source projects. Python has recruited enthusiasts from many professions that use data to
draw conclusions. By learning the Python language, you will join a million‑person‑strong community of software developers and data scientists.
Getting Started. The easiest and recommended way to start writing programs in Python is to log into the companion site for this text,
datahub.berkeley.edu. If you have a @berkeley.edu email address, you already have full access to the programming environment hosted on that site.
You are not at all restricted to using this web‑based programming environment. A Python program can be executed by any computer, regardless of
its manufacturer or operating system, provided that support for the language is installed. If you wish to install the version of Python and its
accompanying libraries that will match this text, we recommend the Anaconda distribution that packages together the Python 3 language interpreter,
IPython libraries, and the Jupyter notebook environment.
This text includes a complete introduction to all of these computational tools. You will learn to write programs, generate images from data, and work
with real‑world data sets that are published online.

1.1.2. Statistical Techniques

The discipline of statistics has long addressed the same fundamental challenge as data science: how to draw robust conclusions about the world
using incomplete information. One of the most important contributions of statistics is a consistent and precise vocabulary for describing the
relationship between observations and conclusions. This text continues in the same tradition, focusing on a set of core inferential problems from
statistics: testing hypotheses, estimating confidence, and predicting unknown quantities.
Data science extends the field of statistics by taking full advantage of computing, data visualization, machine learning, optimization, and access to
information. The combination of fast computers and the Internet gives anyone the ability to access and analyze vast datasets: millions of news
articles, full encyclopedias, databases for any domain, and massive repositories of music, photos, and video.
Applications to real data sets motivate the statistical techniques that we describe throughout the text. Real data often do not follow regular patterns
or match standard equations. The interesting variation in real data can be lost by focusing too much attention on simplistic summaries such as
average values. Computers enable a family of methods based on resampling that apply to a wide range of different inference problems, take into
account all available information, and require few assumptions or conditions. Although these techniques have often been reserved for advanced
courses in statistics, their flexibility and simplicity are a natural fit for data science applications.
1.2. Why Data Science?
Most important decisions are made with only partial information and uncertain outcomes. However, the degree of uncertainty for many decisions can
be reduced sharply by access to large data sets and the computational tools required to analyze them effectively. Data‑driven decision making has
already transformed a tremendous breadth of industries, including finance, advertising, manufacturing, and real estate. At the same time, a wide
range of academic disciplines are evolving rapidly to incorporate large‑scale data analysis into their theory and practice.
Studying data science enables individuals to bring these techniques to bear on their work, their scientific endeavors, and their personal decisions.
Critical thinking has long been a hallmark of a rigorous education, but critiques are often most effective when supported by data. A critical analysis of
any aspect of the world, may it be business or social science, involves inductive reasoning; conclusions can rarely been proven outright, but only
supported by the available evidence. Data science provides the means to make precise, reliable, and quantitative arguments about any set of
observations. With unprecedented access to information and computing, critical thinking about any aspect of the world that can be measured would
be incomplete without effective inferential techniques.
The world has too many unanswered questions and difficult challenges to leave this critical reasoning to only a few specialists. All educated members
of society can build the capacity to reason about data. The tools, techniques, and data sets are all readily available; this text aims to make them
accessible to everyone.

1.3. Plotting the classics

In this example, we will explore statistics for two classic novels: The Adventures of Huckleberry Finn by Mark Twain, and Little Women by Louisa May
Alcott. The text of any book can be read by a computer at great speed. Books published before 1923 are currently in the public domain, meaning that
everyone has the right to copy or use the text in any way. Project Gutenberg is a website that publishes public domain books online. Using Python, we
can load the text of these books directly from the web.
This example is meant to illustrate some of the broad themes of this text. Don’t worry if the details of the program don’t yet make sense. Instead,
focus on interpreting the images generated below. Later sections of the text will describe most of the features of the Python programming language
used below.
First, we read the text of both books into lists of chapters, called huck_finn_chapters and little_women_chapters. In Python, a name cannot
contain any spaces, and so we will often use an underscore _ to stand in for a space. The = in the lines below give a name on the left to the result of
some computation described on the right. A uniform resource locator or URL is an address on the Internet for some content; in this case, the text of a
book. The # symbol starts a comment, which is ignored by the computer but helpful for people reading the code.
# Read two books, fast!

huck_finn_url = 'https://www.inferentialthinking.com/data/huck_finn.txt'
huck_finn_text = read_url(huck_finn_url)
huck_finn_chapters = huck_finn_text.split('CHAPTER ')[44:]

little_women_url = 'https://www.inferentialthinking.com/data/little_women.txt'
little_women_text = read_url(little_women_url)
little_women_chapters = little_women_text.split('CHAPTER ')[1:]

While a computer cannot understand the text of a book, it can provide us with some insight into the structure of the text. The name
huck_finn_chapters is currently bound to a list of all the chapters in the book. We can place them into a table to see how each chapter begins.

# Display the chapters of Huckleberry Finn in a table.

Table().with_column('Chapters', huck_finn_chapters)
Chapters
I. YOU don't know about me without you have read a book ...
II. WE went tiptoeing along a path amongst the trees bac ...
III. WELL, I got a good going‑over in the morning from o ...
IV. WELL, three or four months run along, and it was wel ...
V. I had shut the door to. Then I turned around and ther ...
VI. WELL, pretty soon the old man was up and around agai ...
VII. "GIT up! What you 'bout?" I opened my eyes and look ...
VIII. THE sun was up so high when I waked that I judged ...
IX. I wanted to go and look at a place right about the m ...
X. AFTER breakfast I wanted to talk about the dead man a ...
... (33 rows omitted)
Each chapter begins with a chapter number in Roman numerals, followed by the first sentence of the chapter. Project Gutenberg has printed the first
word of each chapter in upper case.

1.3.1. Literary Characters

The Adventures of Huckleberry Finn describes a journey that Huck and Jim take along the Mississippi River. Tom Sawyer joins them towards the end
as the action heats up. Having loaded the text, we can quickly visualize how many times these characters have each been mentioned at any point in
the book.
# Count how many times the names Jim, Tom, and Huck appear in each chapter.

counts = Table().with_columns([
'Jim', np.char.count(huck_finn_chapters, 'Jim'),
'Tom', np.char.count(huck_finn_chapters, 'Tom'),
'Huck', np.char.count(huck_finn_chapters, 'Huck')
])

# Plot the cumulative counts:

# how many times in Chapter 1, how many times in Chapters 1 and 2, and so on.

cum_counts = counts.cumsum().with_column('Chapter', np.arange(1, 44, 1))

cum_counts.plot(column_for_xticks=3)
plots.title('Cumulative Number of Times Each Name Appears', y=1.08);

In the plot above, the horizontal axis shows chapter numbers and the vertical axis shows how many times each character has been mentioned up to
and including that chapter.
You can see that Jim is a central character by the large number of times his name appears. Notice how Tom is hardly mentioned for much of the book
until he arrives and joins Huck and Jim, after Chapter 30. His curve and Jim’s rise sharply at that point, as the action involving both of them
intensifies. As for Huck, his name hardly appears at all, because he is the narrator.
Little Women is a story of four sisters growing up together during the civil war. In this book, chapter numbers are spelled out and chapter titles are
written in all capital letters.
# The chapters of Little Women, in a table

Table().with_column('Chapters', little_women_chapters)

Chapters
ONE PLAYING PILGRIMS "Christmas won't be Christmas witho ...
TWO A MERRY CHRISTMAS Jo was the first to wake in the gr ...
THREE THE LAURENCE BOY "Jo! Jo! Where are you?" cried Me ...
FOUR BURDENS "Oh, dear, how hard it does seem to take up ...
FIVE BEING NEIGHBORLY "What in the world are you going t ...
SIX BETH FINDS THE PALACE BEAUTIFUL The big house did pr ...
SEVEN AMY'S VALLEY OF HUMILIATION "That boy is a perfect ...
EIGHT JO MEETS APOLLYON "Girls, where are you going?" as ...
NINE MEG GOES TO VANITY FAIR "I do think it was the most ...
TEN THE P.C. AND P.O. As spring came on, a new set of am ...
... (37 rows omitted)
We can track the mentions of main characters to learn about the plot of this book as well. The protagonist Jo interacts with her sisters Meg, Beth, and
Amy regularly, up until Chapter 27 when she moves to New York alone.
# Counts of names in the chapters of Little Women

counts = Table().with_columns([
'Amy', np.char.count(little_women_chapters, 'Amy'),
'Beth', np.char.count(little_women_chapters, 'Beth'),
'Jo', np.char.count(little_women_chapters, 'Jo'),
'Meg', np.char.count(little_women_chapters, 'Meg'),
'Laurie', np.char.count(little_women_chapters, 'Laurie'),

])

# Plot the cumulative counts.

cum_counts = counts.cumsum().with_column('Chapter', np.arange(1, 48, 1))

cum_counts.plot(column_for_xticks=5)
plots.title('Cumulative Number of Times Each Name Appears', y=1.08);
Laurie is a young man who marries one of the girls in the end. See if you can use the plots to guess which one.

1.3.2. Another Kind of Character

In some situations, the relationships between quantities allow us to make predictions. This text will explore how to make accurate predictions based
on incomplete information and develop methods for combining multiple sources of uncertain information to make decisions.
As an example of visualizing information derived from multiple sources, let us first use the computer to get some information that would be tedious to
acquire by hand. In the context of novels, the word “character” has a second meaning: a printed symbol such as a letter or number or punctuation
symbol. Here, we ask the computer to count the number of characters and the number of periods in each chapter of both Huckleberry Finn and Little
Women.
# In each chapter, count the number of all characters;
# call this the "length" of the chapter.
# Also count the number of periods.

chars_periods_huck_finn = Table().with_columns([
'Huck Finn Chapter Length', [len(s) for s in huck_finn_chapters],
'Number of Periods', np.char.count(huck_finn_chapters, '.')
])
chars_periods_little_women = Table().with_columns([
'Little Women Chapter Length', [len(s) for s in little_women_chapters],
'Number of Periods', np.char.count(little_women_chapters, '.')
])

Here are the data for Huckleberry Finn. Each row of the table corresponds to one chapter of the novel and displays the number of characters as well
as the number of periods in the chapter. Not surprisingly, chapters with fewer characters also tend to have fewer periods, in general: the shorter the
chapter, the fewer sentences there tend to be, and vice versa. The relation is not entirely predictable, however, as sentences are of varying lengths
and can involve other punctuation such as question marks.
chars_periods_huck_finn
Huck Finn Chapter Length Number of Periods
7026 66
11982 117
8529 72
6799 84
8166 91
14550 125
13218 127
22208 249
8081 71
7036 70
... (33 rows omitted)
Here are the corresponding data for Little Women.
chars_periods_little_women

Little Women Chapter Length Number of Periods

21759 189
22148 188
20558 231
25526 195
23395 255
14622 140
14431 131
22476 214
33767 337
18508 185
... (37 rows omitted)
You can see that the chapters of Little Women are in general longer than those of Huckleberry Finn. Let us see if these two simple variables – the
length and number of periods in each chapter – can tell us anything more about the two books. One way to do this is to plot both sets of data on the
same axes.
In the plot below, there is a dot for each chapter in each book. Blue dots correspond to Huckleberry Finn and gold dots to Little Women. The
horizontal axis represents the number of periods and the vertical axis represents the number of characters.
plots.figure(figsize=(6, 6))
plots.scatter(chars_periods_huck_finn.column(1),
chars_periods_huck_finn.column(0),
color='darkblue')
plots.scatter(chars_periods_little_women.column(1),
chars_periods_little_women.column(0),
color='gold')
plots.xlabel('Number of periods in chapter')
plots.ylabel('Number of characters in chapter');
The plot shows us that many but not all of the chapters of Little Women are longer than those of Huckleberry Finn, as we had observed by just
looking at the numbers. But it also shows us something more. Notice how the blue points are roughly clustered around a straight line, as are the
yellow points. Moreover, it looks as though both colors of points might be clustered around the same straight line.
Now look at all the chapters that contain about 100 periods. The plot shows that those chapters contain about 10,000 characters to about 15,000
characters, roughly. That’s about 100 to 150 characters per period.
Indeed, it appears from looking at the plot that on average both books tend to have somewhere between 100 and 150 characters between periods, as
a very rough estimate. Perhaps these two great 19th century novels were signaling something so very familiar to us now: the 140‑character limit of
Twitter.

2. Causality and Experiments

“These problems are, and will probably ever remain, among the inscrutable secrets of nature. They belong to a class of questions radically
inaccessible to the human intelligence.” —The Times of London, September 1849, on how cholera is contracted and spread
Does the death penalty have a deterrent effect? Is chocolate good for you? What causes breast cancer?
All of these questions attempt to assign a cause to an effect. A careful examination of data can help shed light on questions like these. In this section
you will learn some of the fundamental concepts involved in establishing causality.
Observation is a key to good science. An observational study is one in which scientists make conclusions based on data that they have observed but
had no hand in generating. In data science, many such studies involve observations on a group of individuals, a factor of interest called a treatment,
and an outcome measured on each individual.
It is easiest to think of the individuals as people. In a study of whether chocolate is good for the health, the individuals would indeed be people, the
treatment would be eating chocolate, and the outcome might be a measure of heart disease. But individuals in observational studies need not be
people. In a study of whether the death penalty has a deterrent effect, the individuals could be the 50 states of the union. A state law allowing the
death penalty would be the treatment, and an outcome could be the state’s murder rate.
The fundamental question is whether the treatment has an effect on the outcome. Any relation between the treatment and the outcome is called an
association. If the treatment causes the outcome to occur, then the association is causal. Causality is at the heart of all three questions posed at the
start of this section. For example, one of the questions was whether chocolate directly causes improvements in health, not just whether there there is
a relation between chocolate and health.
The establishment of causality often takes place in two stages. First, an association is observed. Next, a more careful analysis leads to a decision
about causality.

2.1. Observation and Visualization: John Snow and the Broad Street Pump
One of the most powerful examples of astute observation eventually leading to the establishment of causality dates back more than 150 years. To get
your mind into the right timeframe, try to imagine London in the 1850’s. It was the world’s wealthiest city but many of its people were desperately
poor. Charles Dickens, then at the height of his fame, was writing about their plight. Disease was rife in the poorer parts of the city, and cholera was
among the most feared. It was not yet known that germs cause disease; the leading theory was that “miasmas” were the main culprit. Miasmas
manifested themselves as bad smells, and were thought to be invisible poisonous particles arising out of decaying matter. Parts of London did smell
very bad, especially in hot weather. To protect themselves against infection, those who could afford to held sweet‑smelling things to their noses.
For several years, a doctor by the name of John Snow had been following the devastating waves of cholera that hit England from time to time. The
disease arrived suddenly and was almost immediately deadly: people died within a day or two of contracting it, hundreds could die in a week, and the
total death toll in a single wave could reach tens of thousands. Snow was skeptical of the miasma theory. He had noticed that while entire households
were wiped out by cholera, the people in neighboring houses sometimes remained completely unaffected. As they were breathing the same air—and
miasmas—as their neighbors, there was no compelling association between bad smells and the incidence of cholera.
Snow had also noticed that the onset of the disease almost always involved vomiting and diarrhea. He therefore believed that the infection was
carried by something people ate or drank, not by the air that they breathed. His prime suspect was water contaminated by sewage.
At the end of August 1854, cholera struck in the overcrowded Soho district of London. As the deaths mounted, Snow recorded them diligently, using
a method that went on to become standard in the study of how diseases spread: he drew a map. On a street map of the district, he recorded the
location of each death.
Here is Snow’s original map. Each black bar represents one death. When there are multiple deaths at the same address, the bars corresponding to
those deaths are stacked on top of each other. The black discs mark the locations of water pumps. The map displays a striking revelation—the deaths
are roughly clustered around the Broad Street pump.
Snow studied his map carefully and investigated the apparent anomalies. All of them implicated the Broad Street pump. For example:
There were deaths in houses that were nearer the Rupert Street pump than the Broad Street pump. Though the Rupert Street pump was closer
as the crow flies, it was less convenient to get to because of dead ends and the layout of the streets. The residents in those houses used the
Broad Street pump instead.
There were no deaths in two blocks just east of the pump. That was the location of the Lion Brewery, where the workers drank what they
brewed. If they wanted water, the brewery had its own well.
There were scattered deaths in houses several blocks away from the Broad Street pump. Those were children who drank from the Broad Street
pump on their way to school. The pump’s water was known to be cool and refreshing.
The final piece of evidence in support of Snow’s theory was provided by two isolated deaths in the leafy and genteel Hampstead area, quite far from
Soho. Snow was puzzled by these until he learned that the deceased were Mrs. Susannah Eley, who had once lived in Broad Street, and her niece.
Mrs. Eley had water from the Broad Street pump delivered to her in Hampstead every day. She liked its taste.
Later it was discovered that a cesspit that was just a few feet away from the well of the Broad Street pump had been leaking into the well. Thus the
pump’s water was contaminated by sewage from the houses of cholera victims.
Snow used his map to convince local authorities to remove the handle of the Broad Street pump. Though the cholera epidemic was already on the
wane when he did so, it is possible that the disabling of the pump prevented many deaths from future waves of the disease.
The removal of the Broad Street pump handle has become the stuff of legend. At the Centers for Disease Control (CDC) in Atlanta, when scientists
look for simple answers to questions about epidemics, they sometimes ask each other, “Where is the handle to this pump?”
Snow’s map is one of the earliest and most powerful uses of data visualization. Disease maps of various kinds are now a standard tool for tracking
epidemics.
Towards Causality
Though the map gave Snow a strong indication that the cleanliness of the water supply was the key to controlling cholera, he was still a long way
from a convincing scientific argument that contaminated water was causing the spread of the disease. To make a more compelling case, he had to
use the method of comparison.
Scientists use comparison to identify an association between a treatment and an outcome. They compare the outcomes of a group of individuals who
got the treatment (the treatment group) to the outcomes of a group who did not (the control group). For example, researchers today might compare
the average murder rate in states that have the death penalty with the average murder rate in states that don’t.
If the results are different, that is evidence for an association. To determine causation, however, even more care is needed.

2.2. Snow’s “Grand Experiment”

Encouraged by what he had learned in Soho, Snow completed a more thorough analysis. For some time, he had been gathering data on cholera
deaths in an area of London that was served by two water companies. The Lambeth water company drew its water upriver from where sewage was
discharged into the River Thames. Its water was relatively clean. But the Southwark and Vauxhall (S&V) company drew its water below the sewage
discharge, and thus its supply was contaminated.
The map below shows the areas served by the two companies. Snow honed in on the region where the two service areas overlap.

Snow noticed that there was no systematic difference between the people who were supplied by S&V and those supplied by Lambeth. “Each
company supplies both rich and poor, both large houses and small; there is no difference either in the condition or occupation of the persons
receiving the water of the different Companies … there is no difference whatever in the houses or the people receiving the supply of the two Water
Companies, or in any of the physical conditions with which they are surrounded …”
The only difference was in the water supply, “one group being supplied with water containing the sewage of London, and amongst it, whatever might
have come from the cholera patients, the other group having water quite free from impurity.”
Confident that he would be able to arrive at a clear conclusion, Snow summarized his data in the table below.
Supply Area Number of houses cholera deaths deaths per 10,000 houses
S&V 40,046 1,263 315
Lambeth 26,107 98 37
Rest of London 256,423 1,422 59
The numbers pointed accusingly at S&V. The death rate from cholera in the S&V houses was almost ten times the rate in the houses supplied by
Lambeth.

2.3. Establishing Causality

In the language developed earlier in the section, you can think of the people in the S&V houses as the treatment group, and those in the Lambeth
houses at the control group. A crucial element in Snow’s analysis was that the people in the two groups were comparable to each other, apart from
the treatment.
In order to establish whether it was the water supply that was causing cholera, Snow had to compare two groups that were similar to each other in all
but one aspect—their water supply. Only then would he be able to ascribe the differences in their outcomes to the water supply. If the two groups had
been different in some other way as well, it would have been difficult to point the finger at the water supply as the source of the disease. For example,
if the treatment group consisted of factory workers and the control group did not, then differences between the outcomes in the two groups could
have been due to the water supply, or to factory work, or both. The final picture would have been much more fuzzy.
Snow’s brilliance lay in identifying two groups that would make his comparison clear. He had set out to establish a causal relation between
contaminated water and cholera infection, and to a great extent he succeeded, even though the miasmatists ignored and even ridiculed him. Of
course, Snow did not understand the detailed mechanism by which humans contract cholera. That discovery was made in 1883, when the German
scientist Robert Koch isolated the Vibrio cholerae, the bacterium that enters the human small intestine and causes cholera.
In fact the Vibrio cholerae had been identified in 1854 by Filippo Pacini in Italy, just about when Snow was analyzing his data in London. Because of
the dominance of the miasmatists in Italy, Pacini’s discovery languished unknown. But by the end of the 1800’s, the miasma brigade was in retreat.
Subsequent history has vindicated Pacini and John Snow. Snow’s methods led to the development of the field of epidemiology, which is the study of
the spread of diseases.
Confounding
Let us now return to more modern times, armed with an important lesson that we have learned along the way:
In an observational study, if the treatment and control groups differ in ways other than the treatment, it is difficult to make conclusions
about causality.
An underlying difference between the two groups (other than the treatment) is called a confounding factor, because it might confound you (that is,
mess you up) when you try to reach a conclusion.
Example: Coffee and lung cancer. Studies in the 1960’s showed that coffee drinkers had higher rates of lung cancer than those who did not drink
coffee. Because of this, some people identified coffee as a cause of lung cancer. But coffee does not cause lung cancer. The analysis contained a
confounding factor—smoking. In those days, coffee drinkers were also likely to have been smokers, and smoking does cause lung cancer. Coffee
drinking was associated with lung cancer, but it did not cause the disease.
Confounding factors are common in observational studies. Good studies take great care to reduce confounding and to account for its effects.

2.4. Randomization
An excellent way to avoid confounding is to assign individuals to the treatment and control groups at random, and then administer the treatment to
those who were assigned to the treatment group. Randomization keeps the two groups similar apart from the treatment.
If you are able to randomize individuals into the treatment and control groups, you are running a randomized controlled experiment, also known as a
randomized controlled trial (RCT). Sometimes, people’s responses in an experiment are influenced by their knowing which group they are in. So you
might want to run a blind experiment in which individuals do not know whether they are in the treatment group or the control group. To make this
work, you will have to give the control group a placebo, which is something that looks exactly like the treatment but in fact has no effect.
Randomized controlled experiments have long been a gold standard in the medical field, for example in establishing whether a new drug works. They
are also becoming more commonly used in other fields such as economics.
Example: Welfare subsidies in Mexico. In Mexican villages in the 1990’s, children in poor families were often not enrolled in school. One of the
reasons was that the older children could go to work and thus help support the family. Santiago Levy , a minister in Mexican Ministry of Finance, set
out to investigate whether welfare programs could be used to increase school enrollment and improve health conditions. He conducted an RCT on a
set of villages, selecting some of them at random to receive a new welfare program called PROGRESA. The program gave money to poor families if
their children went to school regularly and the family used preventive health care. More money was given if the children were in secondary school
than in primary school, to compensate for the children’s lost wages, and more money was given for girls attending school than for boys. The
remaining villages did not get this treatment, and formed the control group. Because of the randomization, there were no confounding factors and it
was possible to establish that PROGRESA increased school enrollment. For boys, the enrollment increased from 73% in the control group to 77% in
the PROGRESA group. For girls, the increase was even greater, from 67% in the control group to almost 75% in the PROGRESA group. Due to the
success of this experiment, the Mexican government supported the program under the new name OPORTUNIDADES, as an investment in a healthy
and well educated population.
Benefits of Randomization
In the terminology that we have developed, John Snow conducted an observational study, not a randomized experiment. But he called his study a
“grand experiment” because, as he wrote, “No fewer than three hundred thousand people … were divided into two groups without their choice, and in
most cases, without their knowledge …”
Studies such as Snow’s are sometimes called “natural experiments.” However, true randomization does not simply mean that the treatment and
control groups are selected “without their choice.” Randomization has to be carried out very carefully, following the laws of probability.
The method of randomization can be as simple as tossing a coin. It may also be quite a bit more complex. But every method of randomization
consists of a sequence of carefully defined steps that allow chances to be specified mathematically. This has two important consequences.
1. It allows us to account—mathematically—for the possibility that randomization produces treatment and control groups that are quite different
from each other.
2. It allows us to make precise mathematical statements about differences between the treatment and control groups. This in turn helps us make
justifiable conclusions about whether the treatment has any effect.
What if you can’t randomize?
In some situations it might not be possible to carry out a randomized controlled experiment, even when the aim is to investigate causality. For
example, suppose you want to study the effects of alcohol consumption during pregnancy, and you randomly assign some pregnant women to your
“alcohol” group. You should not expect cooperation from them if you present them with a drink. In such situations you will almost invariably be
conducting an observational study, not an experiment. Be alert for confounding factors.
In this course, you will learn how to conduct and analyze your own randomized experiments. That will involve more detail than has been presented in
this chapter. For now, just focus on the main idea: to try to establish causality, run a randomized controlled experiment if possible. If you are
conducting an observational study, you might be able to establish association but it will be harder to establish causation. Be extremely careful about
confounding factors before making conclusions about causality based on an observational study.

2.5. Terminology and Further Reading

Terminology in this chapter
observational study
treatment
outcome
association
causal association
causality
comparison
treatment group
control group
epidemiology
confounding
randomization
randomized controlled experiment
randomized controlled trial (RCT)
blind
placebo
Fun facts
1. John Snow is sometimes called the father of epidemiology, but he was an anesthesiologist by profession. One of his patients was Queen
Victoria, who was an early recipient of anesthetics during childbirth.
2. Florence Nightingale, the originator of modern nursing practices and famous for her work in the Crimean War, was a die‑hard miasmatist. She
had no time for theories about contagion and germs, and was not one for mincing her words. “There is no end to the absurdities connected with
this doctrine,” she said. “Suffice it to say that in the ordinary sense of the word, there is no proof such as would be admitted in any scientific
enquiry that there is any such thing as contagion.”
3. A later RCT established that the conditions on which PROGRESA insisted—children going to school, preventive health care—were not necessary
to achieve increased enrollment. Just the financial boost of the welfare payments was sufficient.
Good reads
The Strange Case of the Broad Street Pump: John Snow and the Mystery of Cholera by Sandra Hempel, published by our own University of California
Press, reads like a whodunit. It was one of the main sources for this section’s account of John Snow and his work. A word of warning: some of the
contents of the book are stomach‑churning.
Poor Economics, the best seller by Abhijit Banerjee and Esther Duflo of MIT, is an accessible and lively account of ways to fight global poverty. It
includes numerous examples of RCTs, including the PROGRESA example in this chapter. In 2019, Banerjee, Duflo, and Michael Kremer received the
Nobel Prize in Economics, in part for showing that “questions are often best answered via carefully designed experiments.”

3. Programming in Python
Programming can dramatically improve our ability to collect and analyze information about the world, which in turn can lead to discoveries through
the kind of careful reasoning demonstrated in the previous section. In data science, the purpose of writing a program is to instruct a computer to
carry out the steps of an analysis. Computers cannot study the world on their own. People must describe precisely what steps the computer should
take in order to collect and analyze data, and those steps are expressed through programs.

3.1. Expressions
Programming languages are much simpler than human languages. Nonetheless, there are some rules of grammar to learn in any language, and that is
where we will begin. In this text, we will use the Python programming language. Learning the grammar rules is essential, and the same rules used in
the most basic programs are also central to more sophisticated programs.
Programs are made up of expressions, which describe to the computer how to combine pieces of data. For example, a multiplication expression
consists of a * symbol between two numerical expressions. Expressions, such as 3 * 4, are evaluated by the computer. The value (the result of
evaluation) of the last expression in each cell, 12 in this case, is displayed below the cell.
3 * 4

The grammar rules of a programming language are rigid. In Python, the * symbol cannot appear twice in a row. The computer will not try to interpret
an expression that differs from its prescribed expression structures. Instead, it will show a SyntaxError error. The Syntax of a language is its set of
grammar rules, and a SyntaxError indicates that an expression structure doesn’t match any of the rules of the language.
3 * * 4

File "<ipython-input-2-012ea60b41dd>", line 1

3 * * 4
^
SyntaxError: invalid syntax
Small changes to an expression can change its meaning entirely. Below, the space between the *’s has been removed. Because ** appears between
two numerical expressions, the expression is a well‑formed exponentiation expression (the first number raised to the power of the second: 3 times 3
times 3 times 3). The symbols * and ** are called operators, and the values they combine are called operands.
3 ** 4

Common Operators. Data science often involves combining numerical values, and the set of operators in a programming language are designed to
so that expressions can be used to express any sort of arithmetic. In Python, the following operators are essential.
Expression Type Operator Example Value
Addition + 2 + 3 5

Subtraction - 2 - 3 -1

Multiplication * 2 * 3 6

Division / 7 / 3 2.66667

Remainder % 7 % 3 1

Exponentiation 2 0.5 1.41421

Python expressions obey the same familiar rules of precedence as in algebra: multiplication and division occur before addition and subtraction.
Parentheses can be used to group together smaller expressions within a larger expression.
1 + 2 * 3 * 4 * 5 / 6 ** 3 + 7 + 8 - 9 + 10

17.555555555555557

1 + 2 * (3 * 4 * 5 / 6) ** 3 + 7 + 8 - 9 + 10

2017.0

This chapter introduces many types of expressions. Learning to program involves trying out everything you learn in combination, investigating the
behavior of the computer. What happens if you divide by zero? What happens if you divide twice in a row? You don’t always need to ask an expert (or
the Internet); many of these details can be discovered by trying them out yourself.

3.2. Names
Names are given to values in Python using an assignment statement. In an assignment, a name is followed by =, which is followed by any expression.
The value of the expression to the right of = is assigned to the name. Once a name has a value assigned to it, the value will be substituted for that
name in future expressions.
a = 10
b = 20
a + b

A previously assigned name can be used in the expression to the right of =.

quarter = 1/4
half = 2 * quarter
half

0.5

However, only the current value of an expression is assigned to a name. If that value changes later, names that were defined in terms of that value will
not change automatically.
quarter = 4
half

0.5

Names must start with a letter, but can contain both letters and numbers. A name cannot contain a space; instead, it is common to use an underscore
character _ to replace each space. Names are only as useful as you make them; it’s up to the programmer to choose names that are easy to interpret.
Typically, more meaningful names can be invented than a and b. For example, to describe the sales tax on a $5 purchase in Berkeley, CA, the
following names clarify the meaning of the various quantities involved.
purchase_price = 5
state_tax_rate = 0.075
county_tax_rate = 0.02
city_tax_rate = 0
sales_tax_rate = state_tax_rate + county_tax_rate + city_tax_rate
sales_tax = purchase_price * sales_tax_rate
sales_tax

0.475

3.2.1. Example: Growth Rates

The relationship between two measurements of the same quantity taken at different times is often expressed as a growth rate. For example, the
United States federal government employed 2,766,000 people in 2002 and 2,814,000 people in 2012. To compute a growth rate, we must first decide
which value to treat as the initial amount. For values over time, the earlier value is a natural choice. Then, we divide the difference between the
changed and initial amount by the initial amount.

initial = 2766000
changed = 2814000
(changed - initial) / initial

0.01735357917570499

It is also typical to subtract one from the ratio of the two measurements, which yields the same value.
(changed/initial) - 1

0.017353579175704903

This value is the growth rate over 10 years. A useful property of growth rates is that they don’t change even if the values are expressed in different
units. So, for example, we can express the same relationship between thousands of people in 2002 and 2012.
initial = 2766
changed = 2814
(changed/initial) - 1

0.017353579175704903

In 10 years, the number of employees of the US Federal Government has increased by only 1.74%. In that time, the total expenditures of the US
Federal Government increased from $2.37 trillion to $3.38 trillion in 2012.
initial = 2.37
changed = 3.38
(changed/initial) - 1

0.4261603375527425

A 42.6% increase in the federal budget is much larger than the 1.74% increase in federal employees. In fact, the number of federal employees has
grown much more slowly than the population of the United States, which increased 9.21% in the same time period from 287.6 million people in 2002
to 314.1 million in 2012.
initial = 287.6
changed = 314.1
(changed/initial) - 1

0.09214186369958277

A growth rate can be negative, representing a decrease in some value. For example, the number of manufacturing jobs in the US decreased from 15.3
million in 2002 to 11.9 million in 2012, a ‑22.2% growth rate.
initial = 15.3
changed = 11.9
(changed/initial) - 1

-0.2222222222222222

An annual growth rate is a growth rate of some quantity over a single year. An annual growth rate of 0.035, accumulated each year for 10 years, gives
a much larger ten‑year growth rate of 0.41 (or 41%).
1.035 * 1.035 * 1.035 * 1.035 * 1.035 * 1.035 * 1.035 * 1.035 * 1.035 * 1.035 - 1

0.410598760621121

This same computation can be expressed using names and exponents.

annual_growth_rate = 0.035
ten_year_growth_rate = (1 + annual_growth_rate) ** 10 - 1
ten_year_growth_rate

0.410598760621121

Likewise, a ten‑year growth rate can be used to compute an equivalent annual growth rate. Below, t is the number of years that have passed between
measurements. The following computes the annual growth rate of federal expenditures over the last 10 years.
initial = 2.37
changed = 3.38
t = 10
(changed/initial) ** (1/t) - 1

0.03613617208346853

The total growth over 10 years is equivalent to a 3.6% increase each year.
In summary, a growth rate g is used to describe the relative size of an initial amount and a changed amount after some amount of time t. To
compute $changed$, apply the growth rate g repeatedly, t times using exponentiation.
initial * (1 + g) ** t

To compute g, raise the total growth to the power of 1/t and subtract one.
(changed/initial) ** (1/t) - 1

3.3. Call Expressions

Call expressions invoke functions, which are named operations. The name of the function appears first, followed by expressions in parentheses.
abs(-12)

round(5 - 1.3)
4

max(2, 2 + 3, 4)

In this last example, the max function is called on three arguments: 2, 5, and 4. The value of each expression within parentheses is passed to the
function, and the function returns the final value of the full call expression. The max function can take any number of arguments and returns the
maximum.
A few functions are available by default, such as abs and round, but most functions that are built into the Python language are stored in a collection of
functions called a module. An import statement is used to provide access to a module, such as math or operator.
import math
import operator
math.sqrt(operator.add(4, 5))

3.0

An equivalent expression could be expressed using the + and ** operators instead.

(4 + 5) ** 0.5

3.0

Operators and call expressions can be used together in an expression. The percent difference between two values is used to compare values for
which neither one is obviously initial or changed. For example, in 2014 Florida farms produced 2.72 billion eggs while Iowa farms produced 16.25
billion eggs (http://quickstats.nass.usda.gov/). The percent difference is 100 times the absolute value of the difference between the values, divided by
their average. In this case, the difference is larger than the average, and so the percent difference is greater than 100.
florida = 2.72
iowa = 16.25
100*abs(florida-iowa)/((florida+iowa)/2)

142.6462836056932

Learning how different functions behave is an important part of learning a programming language. A Jupyter notebook can assist in remembering the
names and effects of different functions. When editing a code cell, press the tab key after typing the beginning of a name to bring up a list of ways to
complete that name. For example, press tab after math. to see all of the functions available in the math module. Typing will narrow down the list of
options. To learn more about a function, place a ? after its name. For example, typing math.log? will bring up a description of the log function in the
math module.

math.log?

log(x[, base])

Return the logarithm of x to the given base.

If the base not specified, returns the natural logarithm (base e) of x.

The square brackets in the example call indicate that an argument is optional. That is, log can be called with either one or two arguments.
math.log(16, 2)

4.0

math.log(16)/math.log(2)

4.0
The list of Python’s built‑in functions is quite long and includes many functions that are never needed in data science applications. The list of
mathematical functions in the math module is similarly long. This text will introduce the most important functions in context, rather than expecting the
reader to memorize or understand these lists.

3.4. Introduction to Tables

We can now apply Python to analyze data. We will work with data stored in Table structures.
Tables are a fundamental way of representing data sets. A table can be viewed in two ways:
a sequence of named columns that each describe a single attribute of all entries in a data set, or
a sequence of rows that each contain all information about a single individual in a data set.
We will study tables in great detail in the next several chapters. For now, we will just introduce a few methods without going into technical details.
The table cones has been imported for us; later we will see how, but here we will just work with it. First, let’s take a look at it.
cones

Flavor Color Price

strawberry pink 3.55
chocolate light brown 4.75
chocolate dark brown 5.25
strawberry pink 5.25
chocolate dark brown 5.25
bubblegum pink 4.75
The table has six rows. Each row corresponds to one ice cream cone. The ice cream cones are the individuals.
Each cone has three attributes: flavor, color, and price. Each column contains the data on one of these attributes, and so all the entries of any single
column are of the same kind. Each column has a label. We will refer to columns by their labels.
A table method is just like a function, but it must operate on a table. So the call looks like
name_of_table.method(arguments)

For example, if you want to see just the first two rows of a table, you can use the table method show.
cones.show(2)

Flavor Color Price

strawberry pink 3.55
chocolate light brown 4.75
... (4 rows omitted)
You can replace 2 by any number of rows. If you ask for more than six, you will only get six, because cones only has six rows.

3.4.1. Choosing Sets of Columns

The method select creates a new table consisting of only the specified columns.
cones.select('Flavor')
Flavor
strawberry
chocolate
chocolate
strawberry
chocolate
bubblegum
This leaves the original table unchanged.
cones

Flavor Color Price

strawberry pink 3.55
chocolate light brown 4.75
chocolate dark brown 5.25
strawberry pink 5.25
chocolate dark brown 5.25
bubblegum pink 4.75
You can select more than one column, by separating the column labels by commas.
cones.select('Flavor', 'Price')

Flavor Price
strawberry 3.55
chocolate 4.75
chocolate 5.25
strawberry 5.25
chocolate 5.25
bubblegum 4.75
You can also drop columns you don’t want. The table above can be created by dropping the Color column.
cones.drop('Color')

Flavor Price
strawberry 3.55
chocolate 4.75
chocolate 5.25
strawberry 5.25
chocolate 5.25
bubblegum 4.75
You can name this new table and look at it again by just typing its name.
no_colors = cones.drop('Color')

no_colors
Flavor Price
strawberry 3.55
chocolate 4.75
chocolate 5.25
strawberry 5.25
chocolate 5.25
bubblegum 4.75
Like select, the drop method creates a smaller table and leaves the original table unchanged. In order to explore your data, you can create any
number of smaller tables by using choosing or dropping columns. It will do no harm to your original data table.

3.4.2. Sorting Rows

The sort method creates a new table by arranging the rows of the original table in ascending order of the values in the specified column. Here the
cones table has been sorted in ascending order of the price of the cones.

cones.sort('Price')

Flavor Color Price

strawberry pink 3.55
chocolate light brown 4.75
bubblegum pink 4.75
chocolate dark brown 5.25
strawberry pink 5.25
chocolate dark brown 5.25
To sort in descending order, you can use an optional argument to sort. As the name implies, optional arguments don’t have to be used, but they can
be used if you want to change the default behavior of a method.
By default, sort sorts in increasing order of the values in the specified column. To sort in decreasing order, use the optional argument
descending=True.

cones.sort('Price', descending=True)

Flavor Color Price

chocolate dark brown 5.25
strawberry pink 5.25
chocolate dark brown 5.25
bubblegum pink 4.75
chocolate light brown 4.75
strawberry pink 3.55
Like select and drop, the sort method leaves the original table unchanged.

3.4.3. Selecting Rows that Satisfy a Condition

The where method creates a new table consisting only of the rows that satisfy a given condition. In this section we will work with a very simple
condition, which is that the value in a specified column must be equal to a value that we also specify. Thus the where method has two arguments.
The code in the cell below creates a table consisting only of the rows corresponding to chocolate cones.
cones.where('Flavor', 'chocolate')
Flavor Color Price
chocolate light brown 4.75
chocolate dark brown 5.25
chocolate dark brown 5.25
The arguments, separated by a comma, are the label of the column and the value we are looking for in that column. The where method can also be
used when the condition that the rows must satisfy is more complicated. In those situations the call will be a little more complicated as well.
It is important to provide the value exactly. For example, if we specify Chocolate instead of chocolate, then where correctly finds no rows where the
flavor is Chocolate.
cones.where('Flavor', 'Chocolate')

Flavor Color Price

Like all the other table methods in this section, where leaves the original table unchanged.

3.4.4. Example: Salaries in the NBA

“The NBA is the highest paying professional sports league in the world,” reported CNN in March 2016. The table nba contains the salaries of all
National Basketball Association players in 2015‑2016.
Each row represents one player. The columns are:
Column Label Description
PLAYER Player’s name
POSITION Player’s position on team
TEAM Team name
SALARY Player’s salary in 2015‑2016, in millions of dollars
The code for the positions is PG (Point Guard), SG (Shooting Guard), PF (Power Forward), SF (Small Forward), and C (Center). But what follows
doesn’t involve details about how basketball is played.
The first row shows that Paul Millsap, Power Forward for the Atlanta Hawks, had a salary of almost $\$18.7$ million in 2015‑2016.
nba

PLAYER POSITION TEAM SALARY

Klay Thompson SG Golden State Warriors 15.501
Draymond Green PF Golden State Warriors 14.2609
Andrew Bogut C Golden State Warriors 13.8
Andre Iguodala SF Golden State Warriors 11.7105
Stephen Curry PG Golden State Warriors 11.3708
Jason Thompson PF Golden State Warriors 7.00847
Shaun Livingston PG Golden State Warriors 5.54373
Harrison Barnes SF Golden State Warriors 3.8734
Marreese Speights C Golden State Warriors 3.815
Leandro Barbosa SG Golden State Warriors 2.5
Festus Ezeli C Golden State Warriors 2.00875
Brandon Rush SF Golden State Warriors 1.27096
Kevon Looney SF Golden State Warriors 1.13196
Anderson Varejao PF Golden State Warriors 0.289755
The nba table is sorted in alphabetical order of the team names. To see how the players were paid in 2015‑2016, it is useful to sort the data by salary.
Remember that by default, the sorting is in increasing order.
nba.sort('SALARY')
PLAYER POSITION TEAM SALARY
Thanasis Antetokounmpo SF New York Knicks 0.030888
Jordan McRae SG Phoenix Suns 0.049709
Cory Jefferson PF Phoenix Suns 0.049709
Elliot Williams SG Memphis Grizzlies 0.055722
Orlando Johnson SG Phoenix Suns 0.055722
Phil Pressey PG Phoenix Suns 0.055722
Keith Appling PG Orlando Magic 0.061776
Sean Kilpatrick SG Denver Nuggets 0.099418
Erick Green PG Utah Jazz 0.099418
Jeff Ayres PF Los Angeles Clippers 0.111444
... (407 rows omitted)
These figures are somewhat difficult to compare as some of these players changed teams during the season and received salaries from more than
one team; only the salary from the last team appears in the table.
The CNN report is about the other end of the salary scale – the players who were among the highest paid in the world. To identify these players we
can sort in descending order of salary and look at the top few rows.
nba.sort('SALARY', descending=True)

PLAYER POSITION TEAM SALARY

Kobe Bryant SF Los Angeles Lakers 25
Joe Johnson SF Brooklyn Nets 24.8949
LeBron James SF Cleveland Cavaliers 22.9705
Carmelo Anthony SF New York Knicks 22.875
Dwight Howard C Houston Rockets 22.3594
Chris Bosh PF Miami Heat 22.1927
Chris Paul PG Los Angeles Clippers 21.4687
Kevin Durant SF Oklahoma City Thunder 20.1586
Derrick Rose PG Chicago Bulls 20.0931
Dwyane Wade SG Miami Heat 20
... (407 rows omitted)
The late Kobe Bryant was the highest earning NBA player in 2015‑2016.

4. Data Types
Every value has a type, and the built‑in type function returns the type of the result of any expression.
One type we have encountered already is a built‑in function. Python indicates that the type is a builtin_function_or_method; the distinction
between a function and a method is not important at this stage.
type(abs)

builtin_function_or_method

This chapter will explore many useful types of data.

4.1. Numbers
Computers are designed to perform numerical calculations, but there are some important details about working with numbers that every programmer
working with quantitative data should know. Python (like most other programming languages) distinguishes between two different types of numbers:
Integers are called int values in the Python language. They can only represent whole numbers (negative, zero, or positive) that don’t have a
fractional component
Real numbers are called float values (or floating point values) in the Python language. They can represent whole or fractional numbers but
have some limitations.
The type of a number is evident from the way it is displayed: int values have no decimal point and float values always have a decimal point.
# Some int values
2

1 + 3

-1234567890000000000

# Some float values

1.2

3.0

When a float value is combined with an int value using some arithmetic operator, then the result is always a float value. In most cases, two
integers combine to form another integer, but any number (int or float) divided by another will be a float value. Very large or very small float
values are displayed using scientific notation.
1.5 + 2

3.5

3 / 1

3.0

-12345678900000000000.0

-1.23456789e+19

The type function can be used to find the type of any number.
type(3)

int

type(3 / 1)
float

The type of an expression is the type of its final value. So, the type function will never indicate that the type of an expression is a name, because
names are always evaluated to their assigned values.
x = 3
type(x) # The type of x is an int, not a name

int

type(x + 2.5)

float

4.1.1. More About Float Values

Float values are very flexible, but they do have limits.
1. A float can represent extremely large and extremely small numbers. There are limits, but you will rarely encounter them.
2. A float only represents 15 or 16 significant digits for any number; the remaining precision is lost. This limited precision is enough for the vast
majority of applications.
3. After combining float values with arithmetic, the last few digits may be incorrect. Small rounding errors are often confusing when first
encountered.
The first limit can be observed in two ways. If the result of a computation is a very large number, then it is represented as infinite. If the result is a very
small number, then it is represented as zero.
2e306 * 10

2e+307

2e306 * 100

inf

2e-322 / 10

2e-323

2e-322 / 100

0.0

The second limit can be observed by an expression that involves numbers with more than 15 significant digits. These extra digits are discarded before
any arithmetic is carried out.
0.6666666666666666 - 0.6666666666666666123456789

0.0

The third limit can be observed when taking the difference between two expressions that should be equivalent. For example, the expression 2 ** 0.5
computes the square root of 2, but squaring this value does not exactly recover 2.
2 ** 0.5

1.4142135623730951
(2 ** 0.5) * (2 ** 0.5)

2.0000000000000004

(2 ** 0.5) * (2 ** 0.5) - 2

4.440892098500626e-16

The final result above is 0.0000000000000004440892098500626, a number that is very close to zero. The correct answer to this arithmetic expression
is 0, but a small error in the final significant digit appears very different in scientific notation. This behavior appears in almost all programming
languages because it is the result of the standard way that arithmetic is carried out on computers.
Although float values are not always exact, they are certainly reliable and work the same way across all different kinds of computers and
programming languages.

4.2. Strings
Much of the world’s data is text, and a piece of text represented in a computer is called a string. A string can represent a word, a sentence, or even
the contents of every book in a library. Since text can include numbers (like this: 5) or truth values (True), a string can also describe those things.
The meaning of an expression depends both upon its structure and the types of values that are being combined. So, for instance, adding two strings
together produces another string. This expression is still an addition expression, but it is combining a different type of value.
"data" + "science"

'datascience'

Addition is completely literal; it combines these two strings together without regard for their contents. It doesn’t add a space because these are
different words; that’s up to the programmer (you) to specify.
"data" + " " + "science"

'data science'

Single and double quotes can both be used to create strings: 'hi' and "hi" are identical expressions. Double quotes are often preferred because
they allow you to include apostrophes inside of strings.
"This won't work with a single-quoted string!"

"This won't work with a single-quoted string!"

Why not? Try it out.

The str function returns a string representation of any value. Using this function, strings can be constructed that have embedded values.
"That's " + str(1 + 1) + ' ' + str(True)

"That's 2 True"

4.2.1. String Methods

From an existing string, related strings can be constructed using string methods, which are functions that operate on strings. These methods are
called by placing a dot after the string, then calling the function.
For example, the following method generates an uppercased version of a string.
"loud".upper()

'LOUD'

Perhaps the most important method is replace, which replaces all instances of a substring within the string. The replace method takes two
arguments, the text to be replaced and its replacement.
'hitchhiker'.replace('hi', 'ma')

'matchmaker'

String methods can also be invoked using variable names, as long as those names are bound to strings. So, for instance, the following two‑step
process generates the word “degrade” starting from “train” by first creating “ingrain” and then applying a second replacement.
s = "train"
t = s.replace('t', 'ing')
u = t.replace('in', 'de')
u

'degrade'

Note that the line t = s.replace('t', 'ing') doesn’t change the string s, which is still “train”. The method call s.replace('t', 'ing') just has a
value, which is the string “ingrain”.
s

'train'

This is the first time we’ve seen methods, but methods are not unique to strings. As we will see shortly, other types of objects can have them.

4.3. Comparisons
Boolean values most often arise from comparison operators. Python includes a variety of operators that compare values. For example, 3 is larger than
1 + 1.

3 > 1 + 1

True

True
The average of two numbers is always between the smaller number and the larger number. We express this relationship for the numbers x and y
below. You can try different values of x and y to confirm this relationship.
x = 12
y = 5
min(x, y) <= (x+y)/2 <= max(x, y)

True

Strings can also be compared, and their order is alphabetical. A shorter string is less than a longer string that begins with the shorter string.
"Dog" > "Catastrophe" > "Cat"

True

5. Sequences
Values can be grouped together into collections, which allows programmers to organize those values and refer to all of them with a single name. By
grouping values together, we can write code that performs a computation on many pieces of data at once.
Calling the function make_array on several values places them into an array, which is a kind of sequential collection. Below, we collect four different
temperatures into an array called highs. These are the estimated average daily high temperatures over all land on Earth (in degrees Celsius) for the
decades surrounding 1850, 1900, 1950, and 2000, respectively, expressed as deviations from the average absolute high temperature between 1951
and 1980, which was 14.48 degrees.
baseline_high = 14.48
highs = make_array(baseline_high - 0.880, baseline_high - 0.093,
baseline_high + 0.105, baseline_high + 0.684)
highs

array([13.6 , 14.387, 14.585, 15.164])

Collections allow us to pass multiple values into a function using a single name. For instance, the sum function computes the sum of all values in a
collection, and the len function computes its length. (That’s the number of values we put in it.) Using them together, we can compute the average of
a collection.
sum(highs)/len(highs)

14.434000000000001

The complete chart of daily high and low temperatures appears below.

Mean of Daily High Temperature

Mean of Daily Low Temperature

5.1. Arrays
While there are many kinds of collections in Python, we will work primarily with arrays in this class. We’ve already seen that the make_array function
can be used to create arrays of numbers.
Arrays can also contain strings or other types of values, but a single array can only contain a single kind of data. (It usually doesn’t make sense to
group together unlike data anyway.) For example:
english_parts_of_speech = make_array("noun", "pronoun", "verb", "adverb", "adjective",
"conjunction", "preposition", "interjection")
english_parts_of_speech

array(['noun', 'pronoun', 'verb', 'adverb', 'adjective', 'conjunction',

'preposition', 'interjection'], dtype='<U12')

Returning to the temperature data, we create arrays of average daily high temperatures for the decades surrounding 1850, 1900, 1950, and 2000.
baseline_high = 14.48
highs = make_array(baseline_high - 0.880,
baseline_high - 0.093,
baseline_high + 0.105,
baseline_high + 0.684)
highs

array([13.6 , 14.387, 14.585, 15.164])

Arrays can be used in arithmetic expressions to compute over their contents. When an array is combined with a single number, that number is
combined with each element of the array. Therefore, we can convert all of these temperatures to Fahrenheit by writing the familiar conversion
formula.
(9/5) * highs + 32

array([56.48 , 57.8966, 58.253 , 59.2952])

Arrays also have methods, which are functions that operate on the array values. The mean of a collection of numbers is its average value: the sum
divided by the length. Each pair of parentheses in the examples below is part of a call expression; it’s calling a function with no arguments to perform
a computation on the array called highs.
highs.size

highs.sum()

57.736000000000004

highs.mean()

14.434000000000001

5.1.1. Functions on Arrays

The numpy package, abbreviated np in programs, provides Python programmers with convenient and powerful functions for creating and manipulating
arrays.
import numpy as np

For example, the diff function computes the difference between each adjacent pair of elements in an array. The first element of the diff is the
second element minus the first.
np.diff(highs)

array([0.787, 0.198, 0.579])

The full Numpy reference lists these functions exhaustively, but only a small subset are used commonly for data processing applications. These are
grouped into different packages within np. Learning this vocabulary is an important part of learning the Python language, so refer back to this list
often as you work through examples and problems.
However, you don’t need to memorize these. Use this as a reference.
Each of these functions takes an array as an argument and returns a single value.
Function Description
np.prod Multiply all elements together
np.sum Add all elements together
np.all Test whether all elements are true values (non‑zero numbers are true)
np.any Test whether any elements are true values (non‑zero numbers are true)
np.count_nonzero Count the number of non‑zero elements
Each of these functions takes an array as an argument and returns an array of values.
Function Description
np.diff Difference between adjacent elements
np.round Round each number to the nearest integer (whole number)
np.cumprod A cumulative product: for each element, multiply all elements so far

np.cumsum A cumulative sum: for each element, add all elements so far
np.exp Exponentiate each element
np.log Take the natural logarithm of each element
np.sqrt Take the square root of each element
np.sort Sort the elements
Each of these functions takes an array of strings and returns an array.
Function Description
np.char.lower Lowercase each element
np.char.upper Uppercase each element
np.char.strip Remove spaces at the beginning or end of each element
np.char.isalpha Whether each element is only letters (no numbers or symbols)
np.char.isnumeric Whether each element is only numeric (no letters)
Each of these functions takes both an array of strings and a search string; each returns an array.
Function Description
np.char.count Count the number of times a search string appears among the elements of an array
np.char.find The position within each element that a search string is found first
np.char.rfind The position within each element that a search string is found last
np.char.startswith Whether each element starts with the search string

5.2. Ranges
A range is an array of numbers in increasing or decreasing order, each separated by a regular interval. Ranges are useful in a surprisingly large
number of situations, so it’s worthwhile to learn about them.
Ranges are defined using the np.arange function, which takes either one, two, or three arguments: a start, and end, and a ‘step’.
If you pass one argument to np.arange, this becomes the end value, with start=0, step=1 assumed. Two arguments give the start and end with
step=1 assumed. Three arguments give the start, end and step explicitly.

A range always includes its start value, but does not include its end value. It counts up by step, and it stops before it gets to the end.
np.arange(end): An array starting with 0 of increasing consecutive integers, stopping before end.
np.arange(5)

array([0, 1, 2, 3, 4])

Notice how the array starts at 0 and goes only up to 4, not to the end value of 5.
np.arange(start, end): An array of consecutive increasing integers from start, stopping before end.

np.arange(3, 9)

array([3, 4, 5, 6, 7, 8])

np.arange(start, end, step): A range with a difference of step between each pair of consecutive values, starting from start and
stopping before end.

np.arange(3, 30, 5)

array([ 3, 8, 13, 18, 23, 28])

This array starts at 3, then takes a step of 5 to get to 8, then another step of 5 to get to 13, and so on.
When you specify a step, the start, end, and step can all be either positive or negative and may be whole numbers or fractions.
np.arange(1.5, -2, -0.5)

array([ 1.5, 1. , 0.5, 0. , -0.5, -1. , -1.5])

5.2.1. Example: Leibniz’s formula for $\pi$

The great German mathematician and philosopher Gottfried Wilhelm Leibniz (1646 ‑ 1716) discovered a wonderful formula for $\pi$ as an infinite sum
of simple fractions. The formula is
\[\pi = 4 \cdot \left(1 ‑ \frac{1}{3} + \frac{1}{5} ‑ \frac{1}{7} + \frac{1}{9} ‑ \frac{1}{11} + \dots\right)\]
Though some math is needed to establish this, we can use arrays to convince ourselves that the formula works. Let’s calculate the first 5000 terms of
Leibniz’s infinite sum and see if it is close to $\pi$.
\[4 \cdot \left(1 ‑ \frac{1}{3} + \frac{1}{5} ‑ \frac{1}{7} + \frac{1}{9} ‑ \frac{1}{11} + \dots ‑ \frac{1}{9999} \right)\]
We will calculate this finite sum by adding all the positive terms first and then subtracting the sum of all the negative terms [1]:
\[4 \cdot \left( \left(1 + \frac{1}{5} + \frac{1}{9} + \dots + \frac{1}{9997} \right) ‑ \left(\frac{1}{3} + \frac{1}{7} + \frac{1}{11} + \dots + \frac{1}{9999}
\right) \right)\]
The positive terms in the sum have 1, 5, 9, and so on in the denominators. The array by_four_to_20 contains these numbers up to 17:
by_four_to_20 = np.arange(1, 20, 4)
by_four_to_20

array([ 1, 5, 9, 13, 17])

To get an accurate approximation to $\pi$, we’ll use the much longer array positive_term_denominators.
positive_term_denominators = np.arange(1, 10000, 4)
positive_term_denominators

array([ 1, 5, 9, ..., 9989, 9993, 9997])

The positive terms we actually want to add together are just 1 over these denominators:
positive_terms = 1 / positive_term_denominators

The negative terms have 3, 7, 11, and so on on in their denominators. This array is just 2 added to positive_term_denominators.
negative_terms = 1 / (positive_term_denominators + 2)

The overall sum is

4 * ( sum(positive_terms) - sum(negative_terms) )

3.1413926535917955

This is very close to $\pi = 3.14159\dots$. Leibniz’s formula is looking good!

5.2.2. Footnotes
[1] Surprisingly, when we add infinitely many positive and negative fractions, the order can matter! But our approximation to $\pi$ uses only a large
finite number of fractions, so it’s okay to add the terms in any convenient order.

5.3. More on Arrays

It’s often necessary to compute something that involves data from more than one array. If two arrays are of the same size, Python makes it easy to do
calculations involving both arrays.
For our first example, we return once more to the temperature data. This time, we create arrays of average daily high and low temperatures for the
decades surrounding 1850, 1900, 1950, and 2000.
baseline_high = 14.48
highs = make_array(baseline_high - 0.880,
baseline_high - 0.093,
baseline_high + 0.105,
baseline_high + 0.684)
highs

array([13.6 , 14.387, 14.585, 15.164])

baseline_low = 3.00
lows = make_array(baseline_low - 0.872, baseline_low - 0.629,
baseline_low - 0.126, baseline_low + 0.728)
lows

array([2.128, 2.371, 2.874, 3.728])

Suppose we’d like to compute the average daily range of temperatures for each decade. That is, we want to subtract the average daily high in the
1850s from the average daily low in the 1850s, and the same for each other decade.
We could write this laboriously using .item:
make_array(
highs.item(0) - lows.item(0),
highs.item(1) - lows.item(1),
highs.item(2) - lows.item(2),
highs.item(3) - lows.item(3)
)

array([11.472, 12.016, 11.711, 11.436])

As when we converted an array of temperatures from Celsius to Fahrenheit, Python provides a much cleaner way to write this:
highs - lows

array([11.472, 12.016, 11.711, 11.436])

What we’ve seen in these examples are special cases of a general feature of arrays.

5.3.1. Elementwise arithmetic on pairs of numerical arrays

If an arithmetic operator acts on two arrays of the same size, then the operation is performed on each corresponding pair of elements in the two
arrays. The final result is an array.
For example, if array1 and array2 have the same number of elements, then the value of array1 * array2 is an array. Its first element is the first
element of array1 times the first element of array2, its second element is the second element of array1 times the second element of array2, and so
on.

5.3.2. Example: Wallis’ Formula for $\pi$

The number $\pi$ is important in many different areas of math. Centuries before computers were invented, mathematicians worked on finding simple
ways to approximate the numerical value of $\pi$. We have already seen Leibniz’s formula for $\pi$. About half a century before Leibniz, the English
mathematician John Wallis (1616‑1703) also expressed $\pi$ in terms of simple fractions, as an infinite product.
\[ \pi = 2 \cdot \left( \frac{2}{1}\cdot\frac{2}{3}\cdot\frac{4}{3}\cdot\frac{4}{5}\cdot\frac{6}{5}\cdot\frac{6}{7}\dots \right) \]
This is a product of “even/odd” fractions. Let’s use arrays to multiply a million of them, and see if the product is close to $\pi$.
Remember that multiplication can done in any order [1], so we can readjust our calculation to:
\[\pi \approx 2 \cdot \left( \frac{2}{1} \cdot \frac{4}{3} \cdot \frac{6}{5} \cdots \frac{1,000,000}{999999} \right) \cdot \left( \frac{2}{3} \cdot \frac{4}{5}
\cdot \frac{6}{7} \cdots \frac{1,000,000}{1,000,001} \right)\]
We’re now ready to do the calculation. We start by creating an array of even numbers 2, 4, 6, and so on upto 1,000,000. Then we create two lists of
odd numbers: 1, 3, 5, 7, … upto 999,999, and 3, 5, 7, … upto 1,000,001.
even = np.arange(2, 1000001, 2)
one_below_even = even - 1
one_above_even = even + 1

Remember that np.prod multiplies all the elements of an array together. Now we can calculate Wallis’ product, to a good approximation.
2 * np.prod(even/one_below_even) * np.prod(even/one_above_even)

3.1415910827951143

That’s $\pi$ correct to five decimal places. Wallis clearly came up with a great formula.

5.3.3. Footnotes
[1] As we saw in the example about Leibniz’s formula, when we add infinitely many fractions, the order can matter. The same is true with multiplying
fractions, as we are doing here. But our approximation to $\pi$ uses only a large finite number of fractions, so it’s okay to multiply the terms in any
convenient order.

6. Tables
Tables are a fundamental object type for representing data sets. A table can be viewed in two ways:
a sequence of named columns that each describe a single aspect of all entries in a data set, or
a sequence of rows that each contain all information about a single entry in a data set.
In order to use tables, import all of the module called datascience, a module created for this text.
from datascience import *

Empty tables can be created using the Table function. An empty table is useful because it can be extended to contain new rows and columns.
Table()

The with_columns method on a table constructs a new table with additional labeled columns. Each column of a table is an array. To add one new
column to a table, call with_columns with a label and an array. (The with_column method can be used with the same effect.)
Below, we begin each example with an empty table that has no columns.
Table().with_columns('Number of petals', make_array(8, 34, 5))

Number of petals
8
34
5
To add two (or more) new columns, provide the label and array for each column. All columns must have the same length, or an error will occur.
Table().with_columns(
'Number of petals', make_array(8, 34, 5),
'Name', make_array('lotus', 'sunflower', 'rose')
)

Number of petals Name

8 lotus
34 sunflower
5 rose
We can give this table a name, and then extend the table with another column.
flowers = Table().with_columns(
'Number of petals', make_array(8, 34, 5),
'Name', make_array('lotus', 'sunflower', 'rose')
)

flowers.with_columns(
'Color', make_array('pink', 'yellow', 'red')
)

Number of petals Name Color

8 lotus pink
34 sunflower yellow
5 rose red
The with_columns method creates a new table each time it is called, so the original table is not affected. For example, the table flowers still has only
the two columns that it had when it was created.
flowers
Number of petals Name
8 lotus
34 sunflower
5 rose
Creating tables in this way involves a lot of typing. If the data have already been entered somewhere, it is usually possible to use Python to read it into
a table, instead of typing it all in cell by cell.
Often, tables are created from files that contain comma‑separated values. Such files are called CSV files.
Below, we use the Table method read_table to read a CSV file that contains some of the data used by Minard in his graphic about Napoleon’s
Russian campaign. The data are placed in a table named minard.
minard = Table.read_table(path_data + 'minard.csv')
minard

Longitude Latitude City Direction Survivors

32 54.8 Smolensk Advance 145000
33.2 54.9 Dorogobouge Advance 140000
34.4 55.5 Chjat Advance 127100
37.6 55.8 Moscou Advance 100000
34.3 55.2 Wixma Retreat 55000
32 54.6 Smolensk Retreat 24000
30.4 54.4 Orscha Retreat 20000
26.8 54.3 Moiodexno Retreat 12000
We will use this small table to demonstrate some useful Table methods. We will then use those same methods, and develop other methods, on much
larger tables of data.

The Size of the Table

The method num_columns gives the number of columns in the table, and num_rows the number of rows.
minard.num_columns

minard.num_rows

Column Labels
The method labels can be used to list the labels of all the columns. With minard we don’t gain much by this, but it can be very useful for tables that
are so large that not all columns are visible on the screen.
minard.labels

('Longitude', 'Latitude', 'City', 'Direction', 'Survivors')

We can change column labels using the relabeled method. This creates a new table and leaves minard unchanged.
minard.relabeled('City', 'City Name')
Longitude Latitude City Name Direction Survivors
32 54.8 Smolensk Advance 145000
33.2 54.9 Dorogobouge Advance 140000
34.4 55.5 Chjat Advance 127100
37.6 55.8 Moscou Advance 100000
34.3 55.2 Wixma Retreat 55000
32 54.6 Smolensk Retreat 24000
30.4 54.4 Orscha Retreat 20000
26.8 54.3 Moiodexno Retreat 12000
However, this method does not change the original table.
minard

Longitude Latitude City Direction Survivors

32 54.8 Smolensk Advance 145000
33.2 54.9 Dorogobouge Advance 140000
34.4 55.5 Chjat Advance 127100
37.6 55.8 Moscou Advance 100000
34.3 55.2 Wixma Retreat 55000
32 54.6 Smolensk Retreat 24000
30.4 54.4 Orscha Retreat 20000
26.8 54.3 Moiodexno Retreat 12000
A common pattern is to assign the original name minard to the new table, so that all future uses of minard will refer to the relabeled table.
minard = minard.relabeled('City', 'City Name')
minard

Longitude Latitude City Name Direction Survivors

Accessing the Data in a Column

We can use a column’s label to access the array of data in the column.
minard.column('Survivors')

array([145000, 140000, 127100, 100000, 55000, 24000, 20000, 12000])

The 5 columns are indexed 0, 1, 2, 3, and 4. The column Survivors can also be accessed by using its column index.
minard.column(4)

array([145000, 140000, 127100, 100000, 55000, 24000, 20000, 12000])

The 8 items in the array are indexed 0, 1, 2, and so on, up to 7. The items in the column can be accessed using item, as with any array.
minard.column(4).item(0)

145000

minard.column(4).item(5)

24000

Working with the Data in a Column

Because columns are arrays, we can use array operations on them to discover new information. For example, we can create a new column that
contains the percent of all survivors at each city after Smolensk.
initial = minard.column('Survivors').item(0)
minard = minard.with_columns(
'Percent Surviving', minard.column('Survivors')/initial
)
minard

Longitude Latitude City Name Direction Survivors Percent Surviving

32 54.8 Smolensk Advance 145000 1
33.2 54.9 Dorogobouge Advance 140000 0.965517
34.4 55.5 Chjat Advance 127100 0.876552
37.6 55.8 Moscou Advance 100000 0.689655
34.3 55.2 Wixma Retreat 55000 0.37931
32 54.6 Smolensk Retreat 24000 0.165517
30.4 54.4 Orscha Retreat 20000 0.137931
26.8 54.3 Moiodexno Retreat 12000 0.0827586
To make the proportions in the new columns appear as percents, we can use the method set_format with the option PercentFormatter. The
set_format method takes Formatter objects, which exist for dates (DateFormatter), currencies (CurrencyFormatter), numbers, and percentages.

minard.set_format('Percent Surviving', PercentFormatter)

Longitude Latitude City Name Direction Survivors Percent Surviving

32 54.8 Smolensk Advance 145000 100.00%
33.2 54.9 Dorogobouge Advance 140000 96.55%
34.4 55.5 Chjat Advance 127100 87.66%
37.6 55.8 Moscou Advance 100000 68.97%
34.3 55.2 Wixma Retreat 55000 37.93%
32 54.6 Smolensk Retreat 24000 16.55%
30.4 54.4 Orscha Retreat 20000 13.79%
26.8 54.3 Moiodexno Retreat 12000 8.28%

Choosing Sets of Columns

The method select creates a new table that contains only the specified columns.
minard.select('Longitude', 'Latitude')

Longitude Latitude
32 54.8
33.2 54.9
34.4 55.5
37.6 55.8
34.3 55.2
32 54.6
30.4 54.4
26.8 54.3
The same selection can be made using column indices instead of labels.
minard.select(0, 1)

Longitude Latitude
32 54.8
33.2 54.9
34.4 55.5
37.6 55.8
34.3 55.2
32 54.6
30.4 54.4
26.8 54.3
The result of using select is a new table, even when you select just one column.
minard.select('Survivors')

Survivors
145000
140000
127100
100000
55000
24000
20000
12000
Notice that the result is a table, unlike the result of column, which is an array.
minard.column('Survivors')

array([145000, 140000, 127100, 100000, 55000, 24000, 20000, 12000])

Another way to create a new table consisting of a set of columns is to drop the columns you don’t want.
minard.drop('Longitude', 'Latitude', 'Direction')

City Name Survivors Percent Surviving

Smolensk 145000 100.00%
Dorogobouge 140000 96.55%
Chjat 127100 87.66%
Moscou 100000 68.97%
Wixma 55000 37.93%
Smolensk 24000 16.55%
Orscha 20000 13.79%
Moiodexno 12000 8.28%
Neither select nor drop change the original table. Instead, they create new smaller tables that share the same data. The fact that the original table is
preserved is useful! You can generate multiple different tables that only consider certain columns without worrying that one analysis will affect the
other.
minard

Longitude Latitude City Name Direction Survivors Percent Surviving

6.1. Sorting Rows

“The NBA is the highest paying professional sports league in the world,” reported CNN in March 2016. The table nba_salaries contains the salaries
of all National Basketball Association players in 2015‑2016.
Each row represents one player. The columns are:
Column Label Description
PLAYER Player’s name
POSITION Player’s position on team
TEAM Team name
'15-'16 SALARY Player’s salary in 2015‑2016, in millions of dollars

The code for the positions is PG (Point Guard), SG (Shooting Guard), PF (Power Forward), SF (Small Forward), and C (Center). But what follows
doesn’t involve details about how basketball is played.
The first row shows that Paul Millsap, Power Forward for the Atlanta Hawks, had a salary of almost $\$18.7$ million in 2015‑2016.
# This table can be found online: https://www.statcrunch.com/app/index.php?
dataid=1843341
nba_salaries = Table.read_table(path_data + 'nba_salaries.csv')
nba_salaries
PLAYER POSITION TEAM '15‑'16 SALARY
Paul Millsap PF Atlanta Hawks 18.6717
Al Horford C Atlanta Hawks 12
Tiago Splitter C Atlanta Hawks 9.75625
Jeff Teague PG Atlanta Hawks 8
Kyle Korver SG Atlanta Hawks 5.74648
Thabo Sefolosha SF Atlanta Hawks 4
Mike Scott PF Atlanta Hawks 3.33333
Kent Bazemore SF Atlanta Hawks 2
Dennis Schroder PG Atlanta Hawks 1.7634
Tim Hardaway Jr. SG Atlanta Hawks 1.30452
... (407 rows omitted)
The table contains 417 rows, one for each player. Only 10 of the rows are displayed. The show method allows us to specify the number of rows, with
the default (no specification) being all the rows of the table.
nba_salaries.show(3)

PLAYER POSITION TEAM '15‑'16 SALARY

Paul Millsap PF Atlanta Hawks 18.6717
Al Horford C Atlanta Hawks 12
Tiago Splitter C Atlanta Hawks 9.75625
... (414 rows omitted)
Glance through about 20 rows or so, and you will see that the rows are in alphabetical order by team name. It’s also possible to list the same rows in
alphabetical order by player name using the sort method. The argument to sort is a column label or index.
nba_salaries.sort('PLAYER').show(5)

PLAYER POSITION TEAM '15‑'16 SALARY

Aaron Brooks PG Chicago Bulls 2.25
Aaron Gordon PF Orlando Magic 4.17168
Aaron Harrison SG Charlotte Hornets 0.525093
Adreian Payne PF Minnesota Timberwolves 1.93884
Al Horford C Atlanta Hawks 12
... (412 rows omitted)
To examine the players’ salaries, it would be much more helpful if the data were ordered by salary.
To do this, we will first simplify the label of the column of salaries (just for convenience), and then sort by the new label SALARY.
This arranges all the rows of the table in increasing order of salary, with the lowest salary appearing first. The output is a new table with the same
columns as the original but with the rows rearranged.
nba = nba_salaries.relabeled("'15-'16 SALARY", 'SALARY')
nba.sort('SALARY')
PLAYER POSITION TEAM SALARY
Thanasis Antetokounmpo SF New York Knicks 0.030888
Jordan McRae SG Phoenix Suns 0.049709
Cory Jefferson PF Phoenix Suns 0.049709
Elliot Williams SG Memphis Grizzlies 0.055722
Orlando Johnson SG Phoenix Suns 0.055722
Phil Pressey PG Phoenix Suns 0.055722
Keith Appling PG Orlando Magic 0.061776
Sean Kilpatrick SG Denver Nuggets 0.099418
Erick Green PG Utah Jazz 0.099418
Jeff Ayres PF Los Angeles Clippers 0.111444
... (407 rows omitted)
These figures are somewhat difficult to compare as some of these players changed teams during the season and received salaries from more than
one team; only the salary from the last team appears in the table. Point Guard Phil Pressey, for example, moved from Philadelphia to Phoenix during
the year, and might be moving yet again to the Golden State Warriors.
The CNN report is about the other end of the salary scale – the players who are among the highest paid in the world.
To order the rows of the table in decreasing order of salary, we must use sort with the option descending=True.
nba.sort('SALARY', descending=True)

PLAYER POSITION TEAM SALARY

Kobe Bryant SF Los Angeles Lakers 25
Joe Johnson SF Brooklyn Nets 24.8949
LeBron James SF Cleveland Cavaliers 22.9705
Carmelo Anthony SF New York Knicks 22.875
Dwight Howard C Houston Rockets 22.3594
Chris Bosh PF Miami Heat 22.1927
Chris Paul PG Los Angeles Clippers 21.4687
Kevin Durant SF Oklahoma City Thunder 20.1586
Derrick Rose PG Chicago Bulls 20.0931
Dwyane Wade SG Miami Heat 20
... (407 rows omitted)
Kobe Bryant, in his final season with the Lakers, was the highest paid at a salary of $\$25$ million. Notice that the MVP Stephen Curry doesn’t appear
among the top 10. He is quite a bit further down the list, as we will see later.

6.1.1. Named Arguments

The descending=True portion of this call expression is called a named argument. When a function or method is called, each argument has both a
position and a name. Both are evident from the help text of a function or method.
help(nba.sort)
Help on method sort in module datascience.tables:

sort(column_or_label, descending=False, distinct=False) method of

datascience.tables.Table instance
Return a Table of rows sorted according to the values in a column.

Args:
``column_or_label``: the column whose values are used for sorting.

``descending``: if True, sorting will be in descending, rather than

ascending order.

``distinct``: if True, repeated values in ``column_or_label`` will

be omitted.

Returns:
An instance of ``Table`` containing rows sorted based on the values
in ``column_or_label``.

>>> marbles = Table().with_columns(

At the very top of this help text, the signature of the sort method appears:
sort(column_or_label, descending=False, distinct=False)

This describes the positions, names, and default values of the three arguments to sort. When calling this method, you can use either positional
arguments or named arguments, so the following three calls do exactly the same thing.
sort('SALARY', True)
sort('SALARY', descending=True)
sort(column_or_label='SALARY', descending=True)

When an argument is simply True or False, it’s a useful convention to include the argument name so that it’s more obvious what the argument value
means.
6.2. Selecting Rows
Often, we would like to extract just those rows that correspond to entries with a particular feature. For example, we might want only the rows
corresponding to the Warriors, or to players who earned more than $\$10$ million. Or we might just want the top five earners.

6.2.1. Specified Rows

The Table method take does just that – it takes a specified set of rows. Its argument is a row index or array of indices, and it creates a new table
consisting of only those rows.
For example, if we wanted just the first row of nba, we could use take as follows.
nba

PLAYER POSITION TEAM SALARY

Paul Millsap PF Atlanta Hawks 18.6717
This is a new table with just the single row that we specified.
We could also get the fourth, fifth, and sixth rows by specifying a range of indices as the argument.
nba.take(np.arange(3, 6))

PLAYER POSITION TEAM SALARY

Jeff Teague PG Atlanta Hawks 8
Kyle Korver SG Atlanta Hawks 5.74648
Thabo Sefolosha SF Atlanta Hawks 4
If we want a table of the top 5 highest paid players, we can first sort the list by salary and then take the first five rows:
nba.sort('SALARY', descending=True).take(np.arange(5))
PLAYER POSITION TEAM SALARY
Kobe Bryant SF Los Angeles Lakers 25
Joe Johnson SF Brooklyn Nets 24.8949
LeBron James SF Cleveland Cavaliers 22.9705
Carmelo Anthony SF New York Knicks 22.875
Dwight Howard C Houston Rockets 22.3594

6.2.2. Rows Corresponding to a Specified Feature

More often, we will want to access data in a set of rows that have a certain feature, but whose indices we don’t know ahead of time. For example, we
might want data on all the players who made more than $\$10$ million, but we don’t want to spend time counting rows in the sorted table.
The method where does the job for us. Its output is a table with the same columns as the original but only the rows where the feature occurs.
The first argument of where is the label of the column that contains the information about whether or not a row has the feature we want. If the feature
is “made more than $\$10$ million”, the column is SALARY.
The second argument of where is a way of specifying the feature. A couple of examples will make the general method of specification easier to
understand.
In the first example, we extract the data for all those who earned more than $\$10$ million.
nba.where('SALARY', are.above(10))

PLAYER POSITION TEAM SALARY

Paul Millsap PF Atlanta Hawks 18.6717
Al Horford C Atlanta Hawks 12
Joe Johnson SF Brooklyn Nets 24.8949
Thaddeus Young PF Brooklyn Nets 11.236
Al Jefferson C Charlotte Hornets 13.5
Nicolas Batum SG Charlotte Hornets 13.1253
Kemba Walker PG Charlotte Hornets 12
Derrick Rose PG Chicago Bulls 20.0931
Jimmy Butler SG Chicago Bulls 16.4075
Joakim Noah C Chicago Bulls 13.4
... (59 rows omitted)
The use of the argument are.above(10) ensured that each selected row had a value of SALARY that was greater than 10.
There are 69 rows in the new table, corresponding to the 69 players who made more than $10$ million dollars. Arranging these rows in order makes
the data easier to analyze. DeMar DeRozan of the Toronto Raptors was the “poorest” of this group, at a salary of just over $10$ million dollars.
nba.where('SALARY', are.above(10)).sort('SALARY')
PLAYER POSITION TEAM SALARY
DeMar DeRozan SG Toronto Raptors 10.05
Gerald Wallace SF Philadelphia 76ers 10.1059
Luol Deng SF Miami Heat 10.1516
Monta Ellis SG Indiana Pacers 10.3
Wilson Chandler SF Denver Nuggets 10.4494
Brendan Haywood C Cleveland Cavaliers 10.5225
Jrue Holiday PG New Orleans Pelicans 10.5955
Tyreke Evans SG New Orleans Pelicans 10.7346
Marcin Gortat C Washington Wizards 11.2174
Thaddeus Young PF Brooklyn Nets 11.236
... (59 rows omitted)
How much did Stephen Curry make? For the answer, we have to access the row where the value of PLAYER is equal to Stephen Curry. That is placed
a table consisting of just one line:
nba.where('PLAYER', are.equal_to('Stephen Curry'))

PLAYER POSITION TEAM SALARY

Stephen Curry PG Golden State Warriors 11.3708
Curry made just under $\$11.4$ million dollars. That’s a lot of money, but it’s less than half the salary of LeBron James. You’ll find that salary in the
“Top 5” table earlier in this section, or you could find it replacing 'Stephen Curry' by 'LeBron James' in the line of code above.
In the code, are is used again, but this time with the predicate equal_to instead of above. Thus for example you can get a table of all the Warriors:
nba.where('TEAM', are.equal_to('Golden State Warriors')).show()

PLAYER POSITION TEAM SALARY

Danilo Gallinari SF Denver Nuggets 14
Kenneth Faried PF Denver Nuggets 11.236
Wilson Chandler SF Denver Nuggets 10.4494
JJ Hickson C Denver Nuggets 5.6135
Jameer Nelson PG Denver Nuggets 4.345
Will Barton SF Denver Nuggets 3.53333
Emmanuel Mudiay PG Denver Nuggets 3.10224
Darrell Arthur PF Denver Nuggets 2.814
Jusuf Nurkic C Denver Nuggets 1.842
Joffrey Lauvergne C Denver Nuggets 1.70972
... (4 rows omitted)

6.2.3. Multiple Features

You can access rows that have multiple specified features, by using where repeatedly. For example, here is a way to extract all the Point Guards
whose salaries were over $\$15$ million.
nba.where('POSITION', 'PG').where('SALARY', are.above(15))

PLAYER POSITION TEAM SALARY

Derrick Rose PG Chicago Bulls 20.0931
Kyrie Irving PG Cleveland Cavaliers 16.4075
Chris Paul PG Los Angeles Clippers 21.4687
Russell Westbrook PG Oklahoma City Thunder 16.7442
John Wall PG Washington Wizards 15.852

6.2.4. General Form

By now you will have realized that the general way to create a new table by selecting rows with a given feature is to use where and are with the
appropriate condition:
original_table_name.where(column_label_string, are.condition)

nba.where('SALARY', are.between(10, 10.3))

PLAYER POSITION TEAM SALARY

Luol Deng SF Miami Heat 10.1516
Gerald Wallace SF Philadelphia 76ers 10.1059
Danny Green SG San Antonio Spurs 10
DeMar DeRozan SG Toronto Raptors 10.05
Notice that the table above includes Danny Green who made $\$10$ million, but not Monta Ellis who made $\$10.3$ million. As elsewhere in Python,
the range between includes the left end but not the right.
If we specify a condition that isn’t satisfied by any row, we get a table with column labels but no rows.
nba.where('PLAYER', are.equal_to('Barack Obama'))
PLAYER POSITION TEAM SALARY

6.2.5. Some More Conditions

Here are some predicates of are that you might find useful. Note that x and y are numbers, STRING is a string, and Z is either a number or a string; you
have to specify these depending on the feature you want.
Predicate Description
are.equal_to(Z) Equal to Z
are.above(x) Greater than x
are.above_or_equal_to(x) Greater than or equal to x
are.below(x) Less than x
are.below_or_equal_to(x) Less than or equal to x
are.between(x, y) Greater than or equal to x, and less than y
are.strictly_between(x, y) Greater than x and less than y
are.between_or_equal_to(x, y) Greater than or equal to x, and less than or equal to y

are.containing(S) Contains the string S

You can also specify the negation of any of these conditions, by using .not_ before the condition:
Predicate Description
are.not_equal_to(Z) Not equal to Z

are.not_above(x) Not above x

… and so on. The usual rules of logic apply – for example, “not above x” is the same as “below or equal to x”.
We end the section with a series of examples.
The use of are.containing can help save some typing. For example, you can just specify Warriors instead of Golden State Warriors:
nba.where('TEAM', are.containing('Warriors')).show()

PLAYER POSITION TEAM SALARY

Klay Thompson SG Golden State Warriors 15.501
Draymond Green PF Golden State Warriors 14.2609
Andrew Bogut C Golden State Warriors 13.8
Andre Iguodala SF Golden State Warriors 11.7105
Stephen Curry PG Golden State Warriors 11.3708
Jason Thompson PF Golden State Warriors 7.00847
Shaun Livingston PG Golden State Warriors 5.54373
Harrison Barnes SF Golden State Warriors 3.8734
Marreese Speights C Golden State Warriors 3.815
Leandro Barbosa SG Golden State Warriors 2.5
Festus Ezeli C Golden State Warriors 2.00875
Brandon Rush SF Golden State Warriors 1.27096
Kevon Looney SF Golden State Warriors 1.13196
Anderson Varejao PF Golden State Warriors 0.289755
You can extract data for all the guards, both Point Guards and Shooting Guards:
nba.where('POSITION', are.containing('G'))
PLAYER POSITION TEAM SALARY
Jeff Teague PG Atlanta Hawks 8
Kyle Korver SG Atlanta Hawks 5.74648
Dennis Schroder PG Atlanta Hawks 1.7634
Tim Hardaway Jr. SG Atlanta Hawks 1.30452
Jason Richardson SG Atlanta Hawks 0.947276
Lamar Patterson SG Atlanta Hawks 0.525093
Terran Petteway SG Atlanta Hawks 0.525093
Avery Bradley PG Boston Celtics 7.73034
Isaiah Thomas PG Boston Celtics 6.91287
Marcus Smart PG Boston Celtics 3.43104
... (171 rows omitted)
You can get all the players who were not Cleveland Cavaliers and had a salary of no less than $\$20$ million:
other_than_Cavs = nba.where('TEAM', are.not_equal_to('Cleveland Cavaliers'))
other_than_Cavs.where('SALARY', are.not_below(20))

PLAYER POSITION TEAM SALARY

Joe Johnson SF Brooklyn Nets 24.8949
Derrick Rose PG Chicago Bulls 20.0931
Dwight Howard C Houston Rockets 22.3594
Chris Paul PG Los Angeles Clippers 21.4687
Kobe Bryant SF Los Angeles Lakers 25
Chris Bosh PF Miami Heat 22.1927
Dwyane Wade SG Miami Heat 20
Carmelo Anthony SF New York Knicks 22.875
Kevin Durant SF Oklahoma City Thunder 20.1586
The same table can be created in many ways. Here is another, and no doubt you can think of more.
other_than_Cavs.where('SALARY', are.above_or_equal_to(20))

PLAYER POSITION TEAM SALARY

Joe Johnson SF Brooklyn Nets 24.8949
Derrick Rose PG Chicago Bulls 20.0931
Dwight Howard C Houston Rockets 22.3594
Chris Paul PG Los Angeles Clippers 21.4687
Kobe Bryant SF Los Angeles Lakers 25
Chris Bosh PF Miami Heat 22.1927
Dwyane Wade SG Miami Heat 20
Carmelo Anthony SF New York Knicks 22.875
Kevin Durant SF Oklahoma City Thunder 20.1586
As you can see, the use of where with are gives you great flexibility in accessing rows with features that interest you. Don’t hesitate to experiment!

6.3. Example: Population Trends

We are now ready to work with large tables of data. The file below contains “Annual Estimates of the Resident Population by Single Year of Age and
Sex for the United States.” Notice that read_table can read data directly from a URL.
# As of August 2021, this census file is online here:
data = 'http://www2.census.gov/programs-surveys/popest/technical-documentation/file-
layouts/2010-2019/nc-est2019-agesex-res.csv'

# A local copy can be accessed here in case census.gov moves the file:
# data = path_data + 'nc-est2019-agesex-res.csv'

full_census_table = Table.read_table(data)
full_census_table

SEX AGE CENSUS2010POP ESTIMATESBASE2010 POPESTIMATE2010 POPESTIMAT

0 0 3944153 3944160 3951430 396
0 1 3978070 3978090 3957730 396
0 2 4096929 4096939 4090621 397
0 3 4119040 4119051 4111688 410
0 4 4063170 4063186 4077346 41
0 5 4056858 4056872 4064521 408
0 6 4066381 4066412 4072904 40
0 7 4030579 4030594 4042990 40
0 8 4046486 4046497 4025501 40
0 9 4148353 4148369 4125312 40
... (296 rows omitted)
Only the first 10 rows of the table are displayed. Later we will see how to display the entire table; however, this is typically not useful with large tables.
A description of the table appears online.
The SEX column contains numeric codes: 0 stands for the total, 1 for male, and 2 for female. The assumptions underlying this binary categorization
are questionable. We will discuss them in the next section.
In this section we will focus on age and population size.
The AGE column contains ages in completed years, but the special value 999 is a sum of the total population. The “age” 100 too has a special status.
In that category, the Census Bureau includes all people aged 100 or more.
The other columns contain estimates of the US population in each category of sex and age in the years 2010 through 2019. The Census is decennial:
it takes place every 10 years. The most recent Census was held in 2020 and the one before that in 2010. The Census Bureau also estimates
population changes each year. As explained in the Bureau’s description of its methodology, it “adds [the estimated changes] to the last decennial
census to produce updated population estimates every year.”
Typically, a publicly available table will contain more information than necessary for a particular investigation or analysis. To get the large table into a
more usable form, we have to do some data cleaning.
Suppose we are only interested in the population changes from 2014 to 2019. Let’s select the relevant columns.
partial_census_table = full_census_table.select('SEX', 'AGE', 'POPESTIMATE2014',
'POPESTIMATE2019')
partial_census_table
SEX AGE POPESTIMATE2014 POPESTIMATE2019
0 0 3954787 3783052
0 1 3948891 3829599
0 2 3958711 3922044
0 3 4005928 3998665
0 4 4004032 4043323
0 5 4004576 4028281
0 6 4133372 4017227
0 7 4152666 4022319
0 8 4118349 4066194
0 9 4106068 4061874
... (296 rows omitted)
We can simplify the labels of the selected columns.
us_pop = partial_census_table.relabeled('POPESTIMATE2014',
'2014').relabeled('POPESTIMATE2019', '2019')
us_pop

SEX AGE 2014 2019

0 0 3954787 3783052
0 1 3948891 3829599
0 2 3958711 3922044
0 3 4005928 3998665
0 4 4004032 4043323
0 5 4004576 4028281
0 6 4133372 4017227
0 7 4152666 4022319
0 8 4118349 4066194
0 9 4106068 4061874
... (296 rows omitted)

6.3.1. Ages 97‑100

As a warm‑up, let’s examine the total population, labeled by SEX code 0. Since all these rows will have the same value 0 in the SEX column, we will
drop that column.
us_pop_by_age = us_pop.where('SEX', are.equal_to(0)).drop('SEX')
us_pop_by_age
AGE 2014 2019
0 3954787 3783052
1 3948891 3829599
2 3958711 3922044
3 4005928 3998665
4 4004032 4043323
5 4004576 4028281
6 4133372 4017227
7 4152666 4022319
8 4118349 4066194
9 4106068 4061874
... (92 rows omitted)
Now let’s look at the population in the highest ages.
us_pop_by_age.where('AGE', are.between(97, 101))

AGE 2014 2019

97 82948 116969
98 59546 86150
99 41277 57124
100 70685 100322
Not surprisingly, the numbers of people are smaller at higher ages. For example, there are fewer 99‑year‑olds than 98‑year‑olds.
But the numbers for AGE 100 are quite a bit larger than those for age 99. That is because the row with AGE 100 doesn’t just represent 100‑year‑olds. It
also includes those who are older than 100.

6.3.2. Percent Change

Each column of the table us_pop_by_age is an array of the same length, and so columns can be combined using arithmetic. The array below contains
the change in population between 2014 and 2019. There is one entry corresponding to each row of us_pop_by_age.
change = us_pop_by_age.column('2019') - us_pop_by_age.column('2014')
change

array([-171735, -119292, -36667, ..., 15847, 29637, 9938515])

We can augment us_pop_by_age with a column that contains these changes, both in absolute terms and as percents relative to the value in 2014.
us_pop_change = us_pop_by_age.with_columns(
'Change', change,
'Percent Change', change/us_pop_by_age.column('2014')
)
us_pop_change.set_format('Percent Change', PercentFormatter)
AGE 2014 2019 Change Percent Change
0 3954787 3783052 ‑171735 ‑4.34%
1 3948891 3829599 ‑119292 ‑3.02%
2 3958711 3922044 ‑36667 ‑0.93%
3 4005928 3998665 ‑7263 ‑0.18%
4 4004032 4043323 39291 0.98%
5 4004576 4028281 23705 0.59%
6 4133372 4017227 ‑116145 ‑2.81%
7 4152666 4022319 ‑130347 ‑3.14%
8 4118349 4066194 ‑52155 ‑1.27%
9 4106068 4061874 ‑44194 ‑1.08%
... (92 rows omitted)
Almost all the entries displayed in the Percent Change column are negative, demonstrating a drop in population at the youngest ages. However, the
overall population grew by about 9.9 million people, a percent change of just over 3%.
us_pop_change.where('AGE', are.equal_to(999))

AGE 2014 2019 Change Percent Change

999 318301008 328239523 9938515 3.12%
Let us compare this to the change at each age. For ease of interpretation, we will sort the table in decreasing order of the absolute change in
population, contained in the column Change.
us_pop_change.where(
'AGE', are.below(999)
).sort('Change', descending=True)

AGE 2014 2019 Change Percent Change

72 2191642 3191048 999406 45.60%
68 2567511 3345475 777964 30.30%
69 2530460 3252423 721963 28.53%
70 2461426 3136704 675278 27.43%
71 2516392 3083083 566691 22.52%
76 1692960 2222392 529432 31.27%
62 3677408 4156645 479237 13.03%
28 4345247 4818725 473478 10.90%
64 3481789 3950578 468789 13.46%
38 3848856 4305576 456720 11.87%
... (91 rows omitted)
Take a look at the top few rows. While the percent change is about 3% for the overall population, it jumps to well over 20% for the people in their late
sixties and early seventies. This stunning change contributes to what is known as the greying of America.
What could explain this large increase? We can explore this question by examining the years in which the relevant groups were born.
Those who were in the age group 69 to 72 in 2014 were born in the years 1942 to 1945. The attack on Pearl Harbor was in late 1941, and by
1942 U.S. forces were heavily engaged in a massive war that ended in 1945.
Those who were 69 to 72 years old in 2019 were born in the years 1947 to 1950, at the height of the post‑WWII baby boom in the United States.
The post‑war jump in births is a major reason for the large changes that we have observed.
6.4. Example: Sex Ratios
In this section we will continue using the us_pop table from the previous section. But this time we will focus on population trends in relation to the SEX
column.
us_pop

SEX AGE 2014 2019

6.4.1. The Code Used in the SEX Column

The contents of the AGE, 2014, and 2019 columns are straightforward to understand. The AGE column contains ages in completed years. The special
value 999 represents the entire population regardless of age, and 100 represents “100 or more”. The 2014 and 2019 columns contain estimates of the
US population in each of the two years.
The SEX column, however, is more difficult to interpret.
The Census form asks respondents to provide the sex of each household member by checking one of two boxes labeled Male and Female. The SEX
column contains numeric codes: 1 for male, 2 for female, and 0 for the total.
This question has been asked in essentially the same way since 1790. But since then there has been considerable research on whether the sex of
human beings lends itself to simple binary categorization. For example, nonbinary people do not identify exclusively as male or female. A study by the
Williams Institute at the UCLA School of Law in 2021 estimated that at least 1.2 million individuals in the United States identify as nonbinary.
By continuing to use the historical form of the question, the Census fails to reflect the complexity of sex classification. The explanation provided in
the 2020 Census and reproduced in the quotation below does not include instructions for those who do not identify as one of Male or Female.
Responding to the sex question is easy.
A question on sex has been included since the first census in 1790. All 2020 Census questions that involve personal characteristics are
based on self‑identification. When you complete your census, select the box for the biological sex you identify with.
Regardless of the opinion expressed above, responding to this question isn’t easy for everyone. Difficulties with answering the question can lead to
non‑response or inaccurate responses. This can reduce the accuracy of Census data for informing policy decisions and allocating resources.
Before the 2020 Census, the Census Bureau considered revising this question or including broader questions about sexual orientation and gender
identity. In the end the Bureau decided not to change the planned Census.
However, Census Director John Thompson wrote, “The Census Bureau remains committed to reflecting the information needs of our changing
society.” Census forms do change. For example, new questions on race and ethnicity in the 2020 Census have led to a more accurate understanding
of US demographics. We can hope that the 2030 Census will be more inclusive and accurate in all respects.
In what follows, we will use the data provided by the Census keeping in mind the issues described above. We will use the term “male” to mean an
individual for whom “Male” (SEX code 1) was selected on the Census form. We will use “female” to mean an individual for whom “Female” (SEXcode 2)
was selected.
6.4.2. Overall Proportions
We will now begin looking at sex ratios in 2019. First, let’s look at all the age groups together. Remember that this means looking at the rows where
the “age” is coded 999. The table all_ages contains this information. There are three rows: one for the total population, one for males, and one for
females.
us_pop_2019 = us_pop.drop('2014')
all_ages = us_pop_2019.where('AGE', are.equal_to(999))
all_ages

SEX AGE 2019

0 999 328239523
1 999 161657324
2 999 166582199
Row 0 of all_ages contains the total U.S. population in each of the two years. The United States had about 330 million people in 2019.
Row 1 contains the counts for males and Row 2 for females. Compare these two rows to see that in 2019, there were more females than males in the
United States.
The population counts in Row 1 and Row 2 add up to the total population in Row 0.
For comparability with other quantities, we will need to convert these counts to percents out of the total population. Let’s access the total for 2019
and name it. Then, we’ll show a population table with a proportion column. Consistent with our earlier observation that there were more females than
males, 50.75% of the population in 2019 was female and about 49.25% was male.
pop_2019 = all_ages.column('2019').item(0)
all_ages.with_column(
'Proportion', all_ages.column('2019')/pop_2019
).set_format('Proportion', PercentFormatter)

SEX AGE 2019 Proportion

0 999 328239523 100.00%
1 999 161657324 49.25%
2 999 166582199 50.75%

6.4.3. Proportions Among Infants

When we look at infants, however, the opposite is true. Let’s define infants to be babies who have not yet completed one year, represented in the
rows corresponding to AGE 0. Here are their numbers in the population. You can see that male infants outnumbered female infants.
infants = us_pop_2019.where('AGE', are.equal_to(0))
infants

SEX AGE 2019

0 0 3783052
1 0 1935117
2 0 1847935
As before, we can convert these counts to percents out of the total numbers of infants. The resulting table shows that in 2019, just over 51% of
infants in the U.S. were male.
infants_2019 = infants.column('2019').item(0)
infants.with_column(
'Proportion', infants.column('2019')/infants_2019
).set_format('Proportion', PercentFormatter)
SEX AGE 2019 Proportion
0 0 3783052 100.00%
1 0 1935117 51.15%
2 0 1847935 48.85%
In fact, it has long been observed that the proportion of males among newborns is slightly more than 1/2. The reason for this is not thoroughly
understood, and scientists are still working on it.

6.4.4. Sex Ratio at Each Age

We have seen that while there are more male infants than female, there are more females than males in the population overall. That means the split
between sexes must vary across age groups.
To study this variation, we will separate out the data for the females and the males, and eliminate the row where all the ages are aggregated and AGE
is coded as 999.
The tables females and males contain the data for each the two sex codes.
females_all_rows = us_pop_2019.where('SEX', are.equal_to(2))
females = females_all_rows.where('AGE', are.not_equal_to(999))
females

SEX AGE 2019

2 0 1847935
2 1 1871014
2 2 1916500
2 3 1955655
2 4 1976372
2 5 1967081
2 6 1964271
2 7 1966584
2 8 1986471
2 9 1988726
... (91 rows omitted)
males_all_rows = us_pop_2019.where('SEX', are.equal_to(1))
males = males_all_rows.where('AGE', are.not_equal_to(999))
males

SEX AGE 2019

1 0 1935117
1 1 1958585
1 2 2005544
1 3 2043010
1 4 2066951
1 5 2061200
1 6 2052956
1 7 2055735
1 8 2079723
1 9 2073148
... (91 rows omitted)
The plan now is to compare the number of females and the number of males at each age, for each of the two years. Array and Table methods give us
straightforward ways to do this. Both these tables have one row for each age.
males.column('AGE')

array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,

13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77,
78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
91, 92, 93, 94, 95, 96, 97, 98, 99, 100])

females.column('AGE')

array([ 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,

For any given age, we can get the Female:Male sex ratio by dividing the number of females by the number of males.
To do this in one step, we can use column to extract the array of female counts and the corresponding array of male counts, and then simply divide
one array by the other. Elementwise division will create an array of sex ratios for all the years.
ratios = Table().with_columns(
'AGE', females.column('AGE'),
'2019 F:M RATIO', females.column('2019')/males.column('2019')
)
ratios

AGE 2019 F M RATIO

0 0.954947
1 0.955289
2 0.955601
3 0.957242
4 0.956177
5 0.954338
6 0.956801
7 0.956633
8 0.955161
9 0.959278
... (91 rows omitted)
You can see from the display that the ratios are all around 0.96 for children aged nine or younger. When the Female:Male ratio is less than 1, there are
fewer females than males. Thus we are seeing that there were fewer girls than boys in each of the age groups 0, 1, 2, and so on through 9. More
precisely, in each of these age groups there were about 96 girls for every 100 boys.
Then how can the overall proportion of females in the population be higher than the males?
Something quite different happens when we examine the other end of the age range. Here are the Female:Male ratios for people aged more than 75.
ratios.where('AGE', are.above(75)).show()
AGE 2019 F M RATIO
76 1.21422
77 1.23558
78 1.26373
79 1.28129
80 1.29209
81 1.32745
82 1.36101
83 1.39749
84 1.44603
85 1.48588
86 1.53967
87 1.59775
88 1.66125
89 1.73365
90 1.80539
91 1.90275
92 1.99252
93 2.10192
94 2.2271
95 2.34042
96 2.41969
97 2.5868
98 2.65926
99 2.91367
100 3.27411
Not only are all of these ratios greater than 1, signifying more women than men in all of these age groups, many of them are considerably greater than
1.
At ages 92 and 93 the ratios are close to 2, meaning that there were about twice as many women as men at those ages in 2019.
At ages 99 there were about 3 times as many women as men.
If you are wondering how many people there were at these advanced ages, you can use Python to find out:
males.where('AGE', are.contained_in(make_array(92, 93, 99)))

SEX AGE 2019

1 92 131684
1 93 103415
1 99 14596
females.where('AGE', are.contained_in(make_array(92, 93, 99)))

SEX AGE 2019

2 92 262383
2 93 217370
2 99 42528
The graph below shows sex ratios plotted against age. The blue curve shows the 2019 ratios by age.
The ratios are almost 1 (signifying close to equal numbers of males and females) for ages 0 through 60. But they start shooting up dramatically (more
females than males) starting in the 65 to 70 range.
That females outnumber males in the U.S. is partly due to the marked imbalance in favor of women among senior citizens.
ratios.plot('AGE')

7. Visualization
Tables are a powerful way of organizing and visualizing data. However, large tables of numbers can be difficult to interpret, no matter how organized
they are. Sometimes it is much easier to interpret graphs than numbers.
In this chapter we will develop some of the fundamental graphical methods of data analysis. Our source of data is the Internet Movie Database, an
online database that contains information about movies, television shows, video games, and so on. The site Box Office Mojo provides many
summaries of IMDB data, some of which we have adapted. We have also used data summaries from The Numbers, a site with a tagline that says it is
“where data and the movie business meet.”

Scatter Plots and Line Graphs

The table actors contains data on Hollywood actors, both male and female. The columns are:
Column Contents
Actor Name of actor
Total Gross Total gross domestic box office receipt, in millions of dollars, of all of the actor’s movies
Number of Movies The number of movies the actor has been in
Average per Movie Total gross divided by number of movies
#1 Movie The highest grossing movie the actor has been in
Gross Gross domestic box office receipt, in millions of dollars, of the actor’s #1 Movie
In the calculation of the gross receipt, the data tabulators did not include movies where an actor had a cameo role or a speaking role that did not
involve much screen time.
The table has 50 rows, corresponding to the 50 top grossing actors. The table is already sorted by Total Gross, so it is easy to see that Harrison
Ford is the highest grossing actor. At the time when the table was created, his movies had brought in more money at the domestic box office than the
movies of any other actor in the table.
actors = Table.read_table(path_data + 'actors.csv')
actors
Actor Total Number of Average per #1 Movie Gross
Gross Movies Movie
Harrison Ford 4871.7 41 118.8 Star Wars: The Force 936.7
Awakens
Samuel L. 4772.8 69 69.2 The Avengers 623.4
Jackson
Morgan
Freeman 4468.3 61 73.3 The Dark Knight 534.9
Tom Hanks 4340.8 44 98.7 Toy Story 3 415
Robert
Downey, Jr. 3947.3 53 74.5 The Avengers 623.4
Eddie Murphy 3810.4 38 100.3 Shrek 2 441.2
Tom Cruise 3587.2 36 99.6 War of the Worlds 234.3
Johnny Depp 3368.6 45 74.9 Dead Man's Chest 423.3
Michael Caine 3351.5 58 57.8 The Dark Knight 534.9
Scarlett
Johansson 3341.2 37 90.3 The Avengers 623.4
... (40 rows omitted)
Terminology. A variable is a formal name for what we have been calling a “feature” or “attribute”, such as ‘number of movies.’ The term variable
emphasizes the point that a feature can have different values for different individuals. For example, the numbers of movies that actors have been in
vary across all the actors.
Variables that have numerical values and can be measured numerically, such as ‘number of movies’ or ‘average gross receipts per movie’ are called
quantitative or numerical variables.

Scatter Plots
A scatter plot displays the relation between two numerical variables. You saw an example of a scatter plot in an early section where we looked at the
number of periods and number of characters in two classic novels.
The Table method scatter draws a scatter plot consisting of one point for each row of the table. Its first argument is the label of the column to be
plotted on the horizontal axis, and its second argument is the label of the column on the vertical.
actors.scatter('Number of Movies', 'Total Gross')

The plot contains 50 points, one point for each actor in the table. You can see that it slopes upwards, in general. The more movies an actor has been
in, the more the total gross of all of those movies – in general.
Formally, we say that the plot shows an association between the variables, and that the association is positive: high values of one variable tend to be
associated with high values of the other, and low values of one with low values of the other, in general.
Of course there is some variability. Some actors have high numbers of movies but middling total gross receipts. Others have middling numbers of
movies but high receipts. That the association is positive is simply a statement about the broad general trend.
Later in the course we will study how to quantify association. For the moment, we will just think about it qualitatively.
Now that we have explored how the number of movies is related to the total gross receipt, let’s turn our attention to how it is related to the average
gross receipt per movie.
actors.scatter('Number of Movies', 'Average per Movie')

This is a markedly different picture and shows a negative association. In general, the more movies an actor has been in, the less the average receipt
per movie.
Also, one of the points is quite high and off to the left of the plot. It corresponds to one actor who has a low number of movies and high average per
movie. This point is an outlier. It lies outside the general range of the data. Indeed, it is quite far from all the other points in the plot.
We will examine the negative association further by looking at points at the right and left ends of the plot.
For the right end, let’s zoom in on the main body of the plot by just looking at the portion that doesn’t have the outlier.
no_outlier = actors.where('Number of Movies', are.above(10))
no_outlier.scatter('Number of Movies', 'Average per Movie')

The negative association is still clearly visible. Let’s identify the actors corresponding to the points that lie on the right hand side of the plot where the
number of movies is large:
actors.where('Number of Movies', are.above(60))
Actor Total Number of Average per #1 Movie Gross
Gross Movies Movie
Samuel L. 4772.8 69 69.2 The Avengers 623.4
Jackson
Morgan 4468.3 61 73.3 The Dark Knight 534.9
Freeman
Robert DeNiro 3081.3 79 39 Meet the Fockers 279.3
Liam Neeson 2942.7 63 46.7 The Phantom 474.5
Menace
The great actor Robert DeNiro has the highest number of movies and the lowest average receipt per movie. Other fine actors are at points that are
not very far away, but DeNiro’s is at the extreme end.
To understand the negative association, note that the more movies an actor is in, the more variable those movies might be, in terms of style, genre,
and box office draw. For example, an actor might be in some high‑grossing action movies or comedies (such as Meet the Fockers), and also in a large
number of smaller films that may be excellent but don’t draw large crowds. Thus the actor’s value of average receipts per movie might be relatively
low.
To approach this argument from a different direction, let us now take a look at the outlier.
actors.where('Number of Movies', are.below(10))

Actor Gross Total Number of Average per #1 Movie Gross

Movies Movie
Anthony 3162.9 7 451.8 Star Wars: The Force
Daniels Awakens 936.7
As an actor, Anthony Daniels might not have the stature of Robert DeNiro. But his 7 movies had an astonishingly high average receipt of nearly $452$
million dollars per movie.
What were these movies? You might know about the droid C‑3PO in Star Wars:

That’s Anthony Daniels inside the metallic suit. He plays C‑3PO.

Mr. Daniels’ entire filmography (apart from cameos) consists of movies in the high‑grossing Star Wars franchise. That explains both his high average
receipt and his low number of movies.
Variables such as genre and production budget have an effect on the association between the number of movies and the average receipt per movie.
This example is a reminder that studying the association between two variables often involves understanding other related variables as well.

Line Plots
Line plots, sometimes known as line graphs, are among the most common visualizations. They are often used to study chronological trends and
patterns.
The table movies_by_year contains data on movies produced by U.S. studios in each of the years 1980 through 2015. The columns are:
Column Content
Year Year
Total Gross Total domestic box office gross, in millions of dollars, of all movies released
Number of Movies Number of movies released
#1 Movie Highest grossing movie
movies_by_year = Table.read_table(path_data + 'movies_by_year.csv')
movies_by_year

Year Total Gross Number of Movies #1 Movie

2015 11128.5 702 Star Wars: The Force Awakens
2014 10360.8 702 American Sniper
2013 10923.6 688 Catching Fire
2012 10837.4 667 The Avengers
2011 10174.3 602 Harry Potter / Deathly Hallows (P2)
2010 10565.6 536 Toy Story 3
2009 10595.5 521 Avatar
2008 9630.7 608 The Dark Knight
2007 9663.8 631 Spider‑Man 3
2006 9209.5 608 Dead Man's Chest
... (26 rows omitted)
The Table method plot produces a line plot. Its two arguments are the same as those for scatter: first the column on the horizontal axis, then the
column on the vertical. Here is a line plot of the number of movies released each year over the years 1980 through 2015.
movies_by_year.plot('Year', 'Number of Movies')

The graph rises sharply and then has a gentle upwards trend though the numbers vary noticeably from year to year. The sharp rise in the early 1980’s
is due in part to studios returning to the forefront of movie production after some years of filmmaker driven movies in the 1970’s.
Our focus will be on more recent years. In keeping with the theme of movies, the table of rows corresponding to the years 2000 through 2015 have
been assigned to the name century_21.
century_21 = movies_by_year.where('Year', are.above(1999))

century_21.plot('Year', 'Number of Movies')

The global financial crisis of 2008 has a visible effect – in 2009 there is a sharp drop in the number of movies released.
The dollar figures, however, didn’t suffer much.
century_21.plot('Year', 'Total Gross')

The total domestic gross receipt was higher in 2009 than in 2008, even though there was a financial crisis and a much smaller number of movies
were released.
One reason for this apparent contradiction is that people tend to go to the movies when there is a recession. “In Downturn, Americans Flock to the
Movies,” said the New York Times in February 2009. The article quotes Martin Kaplan of the University of Southern California saying, “People want to
forget their troubles, and they want to be with other people.” When holidays and expensive treats are unaffordable, movies provide welcome
entertainment and relief.
In 2009, another reason for high box office receipts was the movie Avatar and its 3D release. Not only was Avatar the #1 movie of 2009, it is also by
some calculations one of the highest grossing movies of all time, as we will see later.
century_21.where('Year', are.equal_to(2009))

Year Total Gross Number of Movies #1 Movie

2009 10595.5 521 Avatar

7.1. Visualizing Categorical Distributions

Data come in many forms that are not numerical. Data can be pieces of music, or places on a map. They can also be categories into which you can
place individuals. Here are some examples of categorical variables.
The individuals are cartons of ice‑cream, and the variable is the flavor in the carton.
The individuals are professional basketball players, and the variable is the player’s team.
The individuals are years, and the variable is the genre of the highest grossing movie of the year.
The individuals are survey respondents, and the variable is the response they choose from among “Not at all satisfied,” “Somewhat satisfied,”
and “Very satisfied.”
The table icecream contains data on 30 cartons of ice‑cream.
icecream = Table().with_columns(
'Flavor', make_array('Chocolate', 'Strawberry', 'Vanilla'),
'Number of Cartons', make_array(16, 5, 9)
)
icecream

Flavor Number of Cartons

Chocolate 16
Strawberry 5
Vanilla 9
The values of the categorical variable “flavor” are chocolate, strawberry, and vanilla.
Each of the cartons had exactly one of the three flavors. In a distribution, each individual belongs to exactly one category and thus has exactly one
value. So we have a distribution of flavors.
The table shows the number of cartons of each flavor. We call this a distribution table. A distribution table shows all the values of the variable along
with the frequency of each one.

7.1.1. Bar Chart

The bar chart is a familiar way of visualizing categorical distributions. It displays a bar for each category. The bars are equally spaced and equally
wide. The length of each bar is proportional to the frequency of the corresponding category.
We will draw bar charts with horizontal bars because it’s easier to label the bars that way. The Table method is therefore called barh. It takes two
arguments: the first is the column label of the categories, and the second is the column label of the frequencies.
icecream.barh('Flavor', 'Number of Cartons')

If the table consists just of a column of categories and a column of frequencies, as in icecream, the method call is even simpler. You can just specify
the column containing the categories, and barh will use the values in the other column as frequencies.
icecream.barh('Flavor')
7.1.2. Design Aspects of Bar Charts
Apart from purely visual differences, there is an important fundamental distinction between bar charts and the two graphs that we saw in the
previous sections. Those were the scatter plot and the line plot, both of which display two quantitative variables – the variables on both axes are
quantitative. In contrast, the bar chart has categories on one axis and numerical quantities on the other.
This has consequences for the chart. First, the width of each bar and the space between consecutive bars is entirely up to the person who is
producing the graph, or to the program being used to produce it. Python made those choices for us. If you were to draw the bar graph by hand, you
could make completely different choices and still have a perfectly correct bar graph, provided you drew all the bars with the same width and kept all
the spaces the same.
Most importantly, the bars can be drawn in any order. The categories “chocolate,” “vanilla,” and “strawberry” have no universal rank order, unlike for
example the numbers 5, 7, and 10.
This means that we can draw a bar chart that is easier to interpret, by rearranging the bars in decreasing order. To do this, we first rearrange the rows
of icecream in decreasing order of Number of Cartons, and then draw the bar chart.
icecream.sort('Number of Cartons', descending=True).barh('Flavor')

This bar chart contains exactly the same information as the previous ones, but it is a little easier to read. While this is not a huge gain in reading a
chart with just three bars, it can be quite significant when the number of categories is large.

7.1.3. Grouping Categorical Data

To construct the table icecream, someone had to look at all 30 cartons of ice‑cream and count the number of each flavor. But if our table does not
already include frequencies, we have to compute the frequencies before we can draw a bar chart. Here is an example where this is necessary.
The table top consists of U.S.A.’s top grossing movies of all time, as of 2017. The first column contains the title of the movie; Star Wars: The Force
Awakens has the top rank, with a box office gross amount of more than 900 million dollars in the United States. The second column contains the
name of the studio that produced the movie. The third contains the domestic box office gross in dollars, and the fourth contains the gross amount
that would have been earned from ticket sales at 2016 prices. The fifth contains the year in which the movie was released.
There are 200 movies on the list. Here are the top ten according to unadjusted gross receipts.
top = Table.read_table(path_data + 'top_movies_2017.csv')
top
Title Studio Gross Gross (Adjusted) Year
Gone with the Wind MGM 198676459 1796176700 1939
Star Wars Fox 460998007 1583483200 1977
The Sound of Music Fox 158671368 1266072700 1965
E.T.: The Extra‑Terrestrial Universal 435110554 1261085000 1982
Titanic Paramount 658672302 1204368000 1997
The Ten Commandments Paramount 65500000 1164590000 1956
Jaws Universal 260000000 1138620700 1975
Doctor Zhivago MGM 111721910 1103564200 1965
The Exorcist Warner Brothers 232906145 983226600 1973
Snow White and the Seven Dwarves Disney 184925486 969010000 1937
... (190 rows omitted)
The studios MGM, Fox, Universal, and Paramount show up more than once in the top ten. Which studios will appear most frequently if we look among
all 200 rows?
To figure this out, first notice that all we need is a table with the movies and the studios; the other information is unnecessary.
movies_and_studios = top.select('Title', 'Studio')

The Table method group allows us to count how frequently each studio appears in the table, by calling each studio a category and collecting all the
rows in each of these new categories.
The group method takes as its argument the label of the column that contains the categories. It returns a table of counts of rows in each category.
Thus group creates a distribution table that shows how the individuals (movies) are distributed among the categories (studios).
The group method lists the categories in ascending order. Since our categories are studio names and therefore represented as strings, ascending
order means alphabetical order.
The column of counts is always called count, but you can change that if you like by using relabeled.
studio_distribution = movies_and_studios.group('Studio')
studio_distribution

Studio count
AVCO 1
Buena Vista 35
Columbia 9
Disney 11
Dreamworks 3
Fox 24
IFC 1
Lionsgate 3
MGM 7
Metro 1
... (13 rows omitted)
The table shows that there are 23 different studios and provides the count of movies released by each one. The total of the count is 200, the total
number of movies.
sum(studio_distribution.column('count'))
200

We can now use this table, along with the graphing skills acquired above, to draw a bar chart that shows which studios are most frequent among the
200 highest grossing movies.
studio_distribution.sort('count', descending=True).barh('Studio')

Buena Vista and Warner Brothers are the most common studios among the top 200 movies. Warner Brothers produces the Harry Potter movies and
Buena Vista produces Star Wars.

7.1.4. Towards Quantitative Variables

Though years are numerical, we could treat the year of release as a categorical variable and plot the its distribution. That is, for every year we could
find how many movies were released that year, and then draw the bar chart of that distribution.
Let’s do that and just look at the 10 earliest years in the distribution.
movies_and_years = top.select('Title', 'Year')
movies_and_years.group('Year').take(np.arange(10)).barh('Year')
The years appear in increasing order because group sorts the categories from lowest to highest. That is important here because years have a
chronological order that has to be maintained. But there is something disquieting about this bar chart. The bars at 1921 and 1937 are just as far apart
from each other as the bars at 1937 and 1939. The bar chart doesn’t show that none of the 200 movies were released in the years 1922 through
1936, nor in 1938. Such inconsistencies and omissions make the distribution in the early years hard to understand based on this visualization.
The distribution of a categorical variable can be displayed using a bar chart. But if the variable is not categorical but quantitative, then the numerical
relations between its values have to be taken into account when we create visualizations. That is the topic of the next section.

7.2. Visualizing Numerical Distributions

Many of the variables that data scientists study are quantitative or numerical. Their values are numbers on which you can perform arithmetic.
Examples that we have seen include the number of periods in chapters of a book, the amount of money made by movies, and the age of people in the
United States.
The values of a categorical variable can be given numerical codes, but that doesn’t make the variable quantitative. In the example in which we studied
Census data broken down by age group, the categorial variable SEX had the numerical codes 1 for ‘Male,’ 2 for ‘Female,’ and 0 for the aggregate of
both groups 1 and 2. While 0, 1, and 2 are numbers, in this context it doesn’t make sense to subtract 1 from 2, or take the average of 0, 1, and 2, or
perform other arithmetic on the three values. SEX is a categorical variable even though the values have been given a numerical code.
For our main example, we will return to a dataset that we studied when we were visualizing categorical data. It is the table top, which consists of data
from U.S.A.’s top grossing movies of all time (as of 2017). For convenience, here is the description of the table again.
The first column contains the title of the movie. The second column contains the name of the studio that produced the movie. The third contains the
domestic box office gross in dollars, and the fourth contains the gross amount that would have been earned from ticket sales at 2016 prices. The fifth
contains the release year of the movie.
There are 200 movies on the list. Here are the top ten according to the unadjusted gross receipts in the column Gross.
top = Table.read_table(path_data + 'top_movies_2017.csv')
# Make the numbers in the Gross and Gross (Adjusted) columns look nicer:
top.set_format([2, 3], NumberFormatter)
Title Studio Gross Gross (Adjusted) Year
Gone with the Wind MGM 198,676,459 1,796,176,700 1939
Star Wars Fox 460,998,007 1,583,483,200 1977
The Sound of Music Fox 158,671,368 1,266,072,700 1965
E.T.: The Extra‑Terrestrial Universal 435,110,554 1,261,085,000 1982
Titanic Paramount 658,672,302 1,204,368,000 1997
The Ten Commandments Paramount 65,500,000 1,164,590,000 1956
Jaws Universal 260,000,000 1,138,620,700 1975
Doctor Zhivago MGM 111,721,910 1,103,564,200 1965
The Exorcist Warner
Brothers 232,906,145 983,226,600 1973
Snow White and the Seven Disney 184,925,486 969,010,000 1937
Dwarves
... (190 rows omitted)
In this section we will draw graphs of the distribution of the numerical variable in the column Gross (Adjusted). For simplicity, let’s create a smaller
table that has the information that we need. And since three‑digit numbers are easier to work with than nine‑digit numbers, let’s measure the
Adjusted Gross receipts in millions of dollars. Note how np.round is used to retain only two decimal places in each entry of the column.

millions = top.select(0).with_columns('Adjusted Gross',

np.round(top.column(3)/1e6, 2))
millions

Title Adjusted Gross

Gone with the Wind 1796.18
Star Wars 1583.48
The Sound of Music 1266.07
E.T.: The Extra‑Terrestrial 1261.08
Titanic 1204.37
The Ten Commandments 1164.59
Jaws 1138.62
Doctor Zhivago 1103.56
The Exorcist 983.23
Snow White and the Seven Dwarves 969.01
... (190 rows omitted)

7.2.1. Binning the Data

Look at the values of the quantitative variable Adjusted Gross. There is likely to be only one movie at each individual value, since the values are being
measured rather finely. It is more interesting to group the values into intervals, known as bins, and see how many movies are in each bin. This process
is called binning.
The counts of individuals (that is, rows) in the bins can be computed using the bin method, analogous to the group method used in the case of
categorical data. The bin method takes as its argument a column label or index, and an optional argument in which you can specify the bins that you
want.
The result is a two‑column table that contains the number of rows in each bin. The first column lists the left endpoints of the bins (but see the note
about the last bin, below).
Let’s try out the method and examine the details of the output. To choose some bins, we will start by looking at the smallest and largest values of
Adjusted Gross.
adj_gross = millions.column('Adjusted Gross')
min(adj_gross), max(adj_gross)

(338.41, 1796.18)

Let’s try bins of width 100, starting at 300 and going to 2000. You are welcome to make other choices. It is common to start with something that
seems reasonable and then adjust based on the results.
bin_counts = millions.bin('Adjusted Gross', bins=np.arange(300,2001,100))
bin_counts.show()

bin Adjusted Gross count

300 68
400 60
500 32
600 15
700 7
800 7
900 3
1000 0
1100 3
1200 3
1300 0
1400 0
1500 1
1600 0
1700 1
1800 0
1900 0
2000 0
Let’s examine Column 0, the bin column. This column specifies the left end of each bin, except in the last row as explained below.
Since the bins split the number line into intervals, they are contiguous. So we must be careful about values at the endpoints. By the usual Python
convention, each bin except the last includes its left endpoint but not its right endpoint.
To make this point, we will use the notation [a, b) to refer to the bin that contains all the values that are greater than or equal to a and strictly less than
b.
To understand the first row of the table, you have to look at the second row as well. These two rows tell us that there were 68 movies in the bin [300,
400). That is, 68 movies had adjusted gross receipts of at least 300 million dollars but less than 400 million dollars.
In general, each element in the Adjusted Gross count column counts all the Adjusted Gross values that are greater than or equal to the value in
bin, but less than the next value in bin.

The last bin: Notice the bin value 2000 in the last row. That’s not the left endpoint of any bin. Instead, it’s the right endpoint of the last bin. This bin
is different from all the others in that it has the form [a, b]. It includes the data at both endpoints. In our example it doesn’t matter because no movie
made 2 billion dollars (that is, 2000 million). But this aspect of binning is important to keep in mind in case you want the bins to end exactly at the
maximum value of the data. All the counts for this last bin appear in the second‑to‑last row, and the count for the last row is always zero.
There are other ways to use the bin method. If you don’t specify any bins, the default is to produce 10 equally wide bins between the minimum and
maximum values of the data. This is often useful for getting a quick sense of the distribution, but the endpoints of the bins tend to be alarming.
millions.bin('Adjusted Gross').show()
bin Adjusted Gross count
338.41 115
484.187 50
629.964 14
775.741 10
921.518 3
1067.3 4
1213.07 2
1358.85 0
1504.63 1
1650.4 1
1796.18 0
You can specify a number of equally wide bins. For example, the option bins=4 leads to 4 equally spaced bins.
millions.bin('Adjusted Gross', bins=4)

bin Adjusted Gross count

338.41 177
702.852 15
1067.3 6
1431.74 2
1796.18 0
But with quantitative data, the bins don’t have to be equally wide. We will see an example of unequal bins later.

7.2.2. Histogram
A histogram is a visualization of the distribution of a quantitative variable. It looks very much like a bar chart but there are some important differences
that we will examine in this section. First, let’s just draw a histogram of the adjusted receipts.
The hist method generates a histogram of the values in a column. The optional unit argument is used in the labels on the two axes. The histogram
below shows the distribution of the adjusted gross amounts, in millions of 2016 dollars. We have not specified the bins, so hist creates 10 equally
wide bins between the minimum and maximum values of the data.
millions.hist('Adjusted Gross', unit="Million Dollars")

This figure has two numerical axes. We will take a quick look at the horizontal axis first, and then examine the vertical axis carefully. For now, just note
that the vertical axis does not represent percents.
7.2.3. The Horizontal Axis
Although in this dataset no movie grossed an amount that is exactly on the edge between two bins, hist does have to account for situations where
there might have been values at the edges. So hist uses the same endpoint convention as the bin method. Bins include the data at their left
endpoint, but not the data at their right endpoint, except for the rightmost bin which includes both endpoints.
We can see that there are 10 bins (some bars are so low that they are hard to see), and that they all have the same width. We can also see that none
of the movies grossed fewer than 300 million dollars; that is because we are considering only the top grossing movies.
It is a little harder to see exactly where the ends of the bins are situated. So it is hard to judge exactly where one bar ends and the next begins.
The optional argument bins can be used with hist to specify the endpoints of the bins exactly as with the bin method. We will start by setting the
numbers in bins to be 300, 400, 500, and so on, ending with 2000.
millions.hist('Adjusted Gross', bins=np.arange(300,2001,100), unit="Million Dollars")

The horizontal axis of this figure is easier to read. For example, you can see exactly where 600 is, even though it is not labeled.
A very small number of movies grossed a billion dollars (1000 million) or more. This results in the figure being skewed to the right, or, less formally,
having a long right hand tail. Distributions of variables like income or rent in large populations also often have this kind of shape.

7.2.4. The Area Principle

Both axes of a histogram are numerical, so you can do arithmetic on both of them. For example, you can multiply the values on either or both of the
axes by a factor. To see how this could affect visual perception, let’s step back from histograms and look at a graphic provided for this purpose by the
site Flowing Data. It is a comparison between the battery sizes of two iPad models.

The larger of the batteries is supposed to be 70% bigger than the smaller. So it’s meant to be bigger but not quite twice as big. However, the larger
battery in the picture looks almost four times the size of the smaller one.
The reason for this problem is that the eye picks up area as the measure of size, not just height or just width. In the picture, both dimensions have
been increased by 70%, leading to a multiplicative effect in the area.
The area principle of visualization says that when we represent a magnitude by a figure that has two dimensions, such as a rectangle, then the area of
the figure should represent the magnitude.
7.2.5. The Histogram: General Principles and Calculation
Histograms follow the area principle and have two defining properties:
1. The bins are drawn to scale and are contiguous (though some might be empty), because the values on the horizontal axis are numerical and
therefore have fixed positions on the number line.
2. The area of each bar is proportional to the number of entries in the bin.
Property 2 is the key to drawing a histogram, and is usually achieved as follows:
\[ \mbox{area of bar} ~=~ \mbox{percent of entries in bin} \]
Since areas represent percents, heights represent something other than percents. The numerical calculation of the heights just uses the fact that the
bar is a rectangle:
\[ \mbox{area of bar} = \mbox{height of bar} \times \mbox{width of bin} \]
and so
\[ \mbox{height of bar} ~=~ \frac{\mbox{area of bar}}{\mbox{width of bin}} ~=~ \frac{\mbox{percent of entries in bin}}{\mbox{width of bin}} \]
The units of height are “percent per unit on the horizontal axis.” The height is the percent in the bin relative to the width of the bin. So it is called
density or crowdedness.
When drawn using this method, the histogram is said to be drawn on the density scale. On this scale:
The area of each bar is equal to the percent of data values that are in the corresponding bin.
The total area of all the bars in the histogram is 100%. In terms of proportions, we can say that the areas of all the bars in a histogram “sum to 1”.

7.2.6. The Vertical Axis: Density Scale

As we have just seen, the height of each bar is the percent of elements that fall into the corresponding bin, relative to the width of the bin. We will
now see how hist calculated the heights of all the bars of the histogram above.
Here is the histogram again for ease of reference.
millions.hist('Adjusted Gross', bins=np.arange(300,2001,100), unit="Million Dollars")

Recall that the table bin_counts has the counts in all the bins of the histogram, specified by bins=np.arange(300, 2000, 100). Also remember that
there are 200 movies in all.
bin_counts.show(3)

bin Adjusted Gross count

300 68
400 60
500 32
... (15 rows omitted)
The [300, 400) bin contains 68 movies. That’s 34% of all the movies:
\[ \mbox{Percent} = \frac{68}{200} \cdot 100 = 34 \]
The width of the [300, 400) bin is $400 ‑ 300 = 100$. So
\[ \mbox{Height} = \frac{34}{100} = 0.34 \]
Units: The height of the bar is 34% divided by 100 million dollars, and so the height is 0.34% per million dollars.
The height of bar is not the percent of entries in the bin. It is the percent of entries in the bin relative to the amount of space in the bin. That is why
the height measures crowdedness or density. The vertical axis is said to be on the density scale.

7.2.7. Why Not Simply Plot the Counts?

The main reason for plotting density on the vertical axis instead of counts or percents is to be able to compare histograms and approximate them
with smooth curves where proportions are represented by areas under the curve.
For example, later in the course you will see histograms that are approximately bell‑shaped. The figure below shows such a shape. The gold shaded
area happens to be 95% of the total area under the curve. Notice that this is quite believeable based on the areas you see in the figure, even though
there are no numbers on the axes. That is why we draw histograms so that areas represent percents.

Drawing histograms on the density scale also allows us to compare histograms that are based on data sets of different sizes or have different choices
of bins. In such cases, neither bin counts nor percents may be directly comparable. But if both histograms are drawn to the density scale then areas
and densities are comparable.
If a histogram has unequal bins, then plotting on the density scale is a requirement for interpretability. For some variables, unequal bins may be
natural. For example, in the U.S. education system, elementary school consists of Grades 1‑5, middle school is Grades 6‑8, high school is Grades 9‑
12, and a Bachelor’s degree takes a further four years. Data on years of education might be binned using these intervals. In fact, no matter what the
variable, bins don’t have to be equal. It is quite common to have one very wide bin towards the left end or right end of the data, where there are not
many values.
Let’s plot a histogram of adjusted gross receipts using unequal bins, and then see what happens if we plot counts instead.
uneven = make_array(300, 350, 400, 500, 1800)
millions.hist('Adjusted Gross', bins=uneven, unit="Million Dollars")

Notice that the [400, 500) bar has the same height (0.3% per million dollars) as in the histograms above.
The areas of the other bars represent the percents in the bins, as usual. The bin method allows us to see the counts in each bin.
millions.bin('Adjusted Gross', bins=uneven)
bin Adjusted Gross count
300 14
350 54
400 60
500 72
1800 0
The [300, 350) bin has only 14 movies whereas the [500, 1800] bin has 72 movies. But the bar over the [500, 1800] bin is much shorter than the bar
over [300, 350). The [500, 1800] bin is so wide that its 72 movies are much less crowded than the 14 movies in the narrow [300, 350) bin. In other
words, there is less density over the [500, 1800] interval.
If instead you just plot the counts using the normed=False option as shown below, the figure looks completely different and misrepresents the data.
millions.hist('Adjusted Gross', bins=uneven, normed=False)

Even though hist has been used, the figure above is NOT A HISTOGRAM. It misleadingly exaggerates the movies grossing at least 500 million
dollars. The height of each bar is simply plotted at the number of movies in the bin, without accounting for the difference in the widths of the bins. In
this count‑based figure, the shape of the distribution of movies is lost entirely.

7.2.8. Flat Tops and the Level of Detail

Even though the density scale correctly represents percents using area, some detail is lost by grouping values into bins.
Take another look at the [400, 500) bin in the figure below. The flat top of the bar, at the level 0.3% per million dollars, hides the fact that the movies
are somewhat unevenly distributed across that bin.
millions.hist('Adjusted Gross', bins=uneven, unit="Million Dollars")

To see this, let us split the [400, 500) bin into 10 narrower bins, each of width 10 million dollars.
some_tiny_bins = make_array(
300, 350, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 1800)
millions.hist('Adjusted Gross', bins=some_tiny_bins, unit='Million Dollars')
Some of the skinny bars are taller than 0.3 and others are shorter. By putting a flat top at the level 0.3 across the whole bin, we are deciding to ignore
the finer detail and are using the flat level as a rough approximation. Often, though not always, this is sufficient for understanding the general shape
of the distribution.
The height as a rough approximation. This observation gives us a different way of thinking about the height. Look again at the [400, 500) bin in the
earlier histograms. As we have seen, the bin is 100 million dollars wide and contains 30% of the data. Therefore the height of the corresponding bar is
0.3% per million dollars.
Now think of the bin as consisting of 100 narrow bins that are each 1 million dollars wide. The bar’s height of “0.3% per million dollars” means that as
a rough approximation, 0.3% of the movies are in each of those 100 skinny bins of width 1 million dollars.
We have the entire dataset that is being used to draw the histograms. So we can draw the histograms to as fine a level of detail as the data and our
patience will allow. Smaller bins will lead to a more detailed picture. However, if you are looking at a histogram in a book or on a website, and you
don’t have access to the underlying dataset, then it becomes important to have a clear understanding of the “rough approximation” created by the
flat tops.

7.2.9. Computing All Heights

We know how to find the height of each histogram bar. Let’s use that to develop code that computes all the heights at once.
We will use the histogram below as our example. The bins are specified in the array uneven.
millions.hist('Adjusted Gross', bins=uneven, unit="Million Dollars")

We will start by getting the counts in the bins.

histogram_elements = millions.bin('Adjusted Gross', bins=uneven).relabeled(1, 'count')
histogram_elements
bin count
300 14
350 54
400 60
500 72
1800 0
We can now add a column containing the percent in each bin.
total_count = sum(histogram_elements.column('count'))
percents = np.round(100*histogram_elements.column('count')/total_count, 2)
histogram_elements = histogram_elements.with_columns('percent', percents)
histogram_elements

bin count percent

300 14 7
350 54 27
400 60 30
500 72 36
1800 0 0
Column 0 contains the left ends of all the bins, except for its last element which is the right end of the last bin. So we can use np.diff to find the
widths of all the bins. Then we will add the widths to the histogram_elements table, by first removing the last row.
bin_widths = np.diff(histogram_elements.column('bin'))
num_bins = histogram_elements.num_rows - 1 # the number of bins
histogram_elements = histogram_elements.take(
np.arange(num_bins)).with_columns(
'width', bin_widths
)
histogram_elements

bin count percent width

300 14 7 50
350 54 27 50
400 60 30 100
500 72 36 1300
Finally, we can add a column of heights.
heights = np.round(
histogram_elements.column('percent')/histogram_elements.column('width'),2)
histogram_elements = histogram_elements.with_columns('height', heights)
histogram_elements

bin count percent width height

300 14 7 50 0.14
350 54 27 50 0.54
400 60 30 100 0.3
500 72 36 1300 0.03
Here is the histogram again for convenience. Compare it with the table above to confirm that the calculation of heights looks good.
millions.hist('Adjusted Gross', bins=uneven)
7.2.10. Differences Between Bar Charts and Histograms
Bar charts display one numerical quantity per category. They are often used to display the distributions of categorical variables. Histograms
display the distributions of quantitative variables.
All the bars in a bar chart have the same width, and there is an equal amount of space between consecutive bars. The bars can be in any order
because the distribution is categorical. The bars of a histogram are contiguous; the bins are drawn to scale on the number line.
The lengths (or heights, if the bars are drawn vertically) of the bars in a bar chart are proportional to the count in each category. The heights of
bars in a histogram measure densities; the areas of bars in a histogram are proportional to the counts in the bins.

7.3. Overlaid Graphs

In this chapter, we have learned how to visualize data by drawing graphs. A common use of such visualizations is to compare two datasets. In this
section, we will see how to overlay plots, that is, draw them in a single graphic on a common pair of axes.
For the overlay to make sense, the graphs that are being overlaid must represent the same variables and be measured in the same units.
To draw overlaid graphs, the methods scatter, plot, and barh can all be called in the same way. For scatter and plot, one column must serve as
the common horizontal axis for all the overlaid graphs. For barh, one column must serve as the common axis which is the set of categories. The
general call looks like:
name_of_table.method(column_label_of_common_axis, array_of_labels_of_variables_to_plot)

More commonly, we will first select only the columns needed for our graph, and then call the method by just specifying the variable on the common
axis:
name_of_table.method(column_label_of_common_axis)

7.3.1. Overlaid Scatter Plots

The table sons_heights is part of a historical data set on the heights of parents and their children. Specifically, the population consists of 179 men
who were the first‑born in their families. The data are their own heights and the heights of their parents. All heights were measured in inches.
sons_heights = Table.read_table(path_data + 'sons_heights.csv')
sons_heights
father mother son
78.5 67 73.2
75.5 66.5 73.5
75 64 71
75 64 70.5
75 58.5 72
74 68 76.5
74 62 74
73 67 71
73 67 68
73 66.5 71
... (169 rows omitted)
The scatter method allows us to visualize how the sons’ heights are related to the heights of both their parents. In the graph, the sons’ heights will
form the common horizontal axis.
sons_heights.scatter('son')

Notice how we only specified the variable (sons’ heights) on the common horizontal axis. Python drew two scatter plots: one each for the relation
between this variable and the other two.
Each point represents a row of the table, that is, a “father, mother, son” trio. For all points, the horizontal axis represents the son’s height. In the blue
points, the vertical axis represents the father’s height. In the gold points, the vertical axis represents the mother’s heights.
Both the gold and the blue scatter plots slope upwards and show a positive association between the sons’ heights and the heights of both their
parents. The blue (fathers) plot is in general higher than the gold, because the fathers were in general taller than the mothers.

7.3.2. Overlaid Line Plots

Our next example involves data on children of more recent times. We will return to the Census data table us_pop, created below again for reference.
From this table, we will extract the counts of all children in each of the age categories 0 through 18 years.
# Read the full Census table
data = 'http://www2.census.gov/programs-surveys/popest/technical-documentation/file-
layouts/2010-2019/nc-est2019-agesex-res.csv'
full_census_table = Table.read_table(data)

# Select columns from the full table and relabel some of them
partial_census_table = full_census_table.select('SEX', 'AGE', 'POPESTIMATE2014',
'POPESTIMATE2019')
us_pop = partial_census_table.relabeled('POPESTIMATE2014',
'2014').relabeled('POPESTIMATE2019', '2019')

# Access the rows corresponding to all children, ages 0-18

children = us_pop.where('SEX', are.equal_to(0)).where('AGE', are.below(19)).drop('SEX')
children.show()

AGE 2014 2019

0 3954787 3783052
1 3948891 3829599
2 3958711 3922044
3 4005928 3998665
4 4004032 4043323
5 4004576 4028281
6 4133372 4017227
7 4152666 4022319
8 4118349 4066194
9 4106068 4061874
10 4114558 4060940
11 4084457 4189261
12 4067187 4208387
13 4168095 4175221
14 4231353 4164459
15 4162828 4175459
16 4165925 4150420
17 4181940 4142425
18 4221344 4255827
We can now draw two overlaid line plots, showing the numbers of children in the different age groups for each of the years 2014 and 2019. The call is
analogous to the scatter call in the previous example.
children.plot('AGE')
Though the horizontal axis labels include some half‑integers, it’s important to remember that we only have data at ages 0, 1, 2, and so on. The line
plots “join the dots” in between.
The two graphs cross each other in a few places. For example, there were more 6‑year‑olds in 2014 than in 2019, and there were more 12‑year‑olds
in 2019 than in 2014.
Of course, the 12‑year‑olds in 2019 mostly consist of the children who were 7‑year‑olds in 2014. To see this on the plots, compare the gold graph at
AGE 12 and the blue graph at AGE 7. You will notice that the gold graph (2019) looks very much like the blue graph (2014) slid over to the right by 5
years. The slide is accompanied by a slight rise due to the net effect of children who entered the country between 2014 and 2019 outnumbering
those who left. Fortunately at these ages there is not much loss of life.

7.3.3. Bar Charts

The Kaiser Family Foundation has complied Census data on the distribution of race and ethnicity in the U.S. The Foundation’s website provides
compilations of data for the entire U.S. population in 2019, as well as for U.S. children who were younger than 18 years old that year.
The table usa_ca is adapted from their data for the United States and California. The columns represent everyone in the U.S.A., everyone in California,
children in the U.S.A., and children in California.
The body of the table contains percents in the different categories. Each column shows the distribution of the Ethnicity/Race variable in the group
of people corresponding to that column. So in each column, the entries add up to 100. The API category consists of Asians and Pacific Islanders
including Native Hawaiians. The Other category includes Native Americans, Alaskan natives, and people who identify with multiple races.
usa_ca = Table.read_table(path_data + 'usa_ca_2019.csv')
usa_ca

Ethnicity/Race USA All CA All USA Children CA Children

API 5.8 15.1 4.9 11.5
Black 12.2 5.3 13.4 4.9
Hispanic 18.5 39.5 25.6 52.1
White 60.1 36.4 50 25.5
Other 3.4 3.7 6.1 6
It is natural to want to compare these distributions. It makes sense to compare the columns directly, because all the entries are percents and are
therefore on the same scale.
The method barh allows us to visualize the comparisons by drawing multiple bar charts on the same axes. The call is analogous to those for scatter
and plot: we have to specify the common axis of categories.
usa_ca.barh('Ethnicity/Race')
While drawing the overlaid bar charts is straightforward, there is a bit too much information on this graph for us to be able to sort out similarities and
differences between populations. It is much easier to compare the populations one pair at a time.
Let’s start by comparing the entire populations of the U.S.A. and California.
usa_ca.select('Ethnicity/Race', 'USA All', 'CA All').barh('Ethnicity/Race')

The two distributions are quite different. California has higher percents in the API and Hispanic categories, and correspondingly lower percents in
theBlack and White categories. The percents in the Other category are quite similar in the two populations. The differences are largely due to
California’s geographical location and patterns of immigration and migration, both historically and in more recent decades.
As you can see from the graph, almost 40% of the Californian population in 2019 was Hispanic. A comparison with the population of children in the
state indicates that the Hispanic proportion is likely to be greater in future years. Among Californian children in 2019, more than 50% were in the
Hispanic category.

usa_ca.select('Ethnicity/Race', 'CA All', 'CA Children').barh('Ethnicity/Race')

More complex data sets naturally give rise to varied and interesting visualizations, including overlaid graphs of different kinds. To analyze such data, it
helps to have some more skills in data manipulation, so that we can get the data into a form that allows us to use methods like those in this section. In
the next chapter we will develop some of these skills.

8. Functions and Tables

We are building up a useful inventory of techniques for identifying patterns and themes in a data set by using functions already available in Python.
We will now explore a core feature of the Python programming language: function definition.
We have used functions extensively already in this text, but never defined a function of our own. The purpose of defining a function is to give a name
to a computational process that may be applied multiple times. There are many situations in computing that require repeated computation. For
example, it is often the case that we want to perform the same manipulation on every value in a column of a table.

Defining a Function
The definition of the double function below simply doubles a number.
# Our first function definition

def double(x):
""" Double x """
return 2*x

We start any function definition by writing def. Here is a breakdown of the other parts (the syntax) of this small function:

When we run the cell above, no particular number is doubled, and the code inside the body of double is not yet evaluated. In this respect, our
function is analogous to a recipe. Each time we follow the instructions in a recipe, we need to start with ingredients. Each time we want to use our
function to double a number, we need to specify a number.
We can call double in exactly the same way we have called other functions. Each time we do that, the code in the body is executed, with the value of
the argument given the name x.
double(17)

34
double(-0.6/4)

-0.3

The two expressions above are both call expressions. In the second one, the value of the expression -0.6/4 is computed and then passed as the
argument named x to the double function. Each call expresson results in the body of double being executed, but with a different value of x.
The body of double has only a single line:
return 2*x

Executing this return statement completes execution of the double function’s body and computes the value of the call expression.
The argument to double can be any expression, as long as its value is a number. For example, it can be a name. The double function does not know
or care how its argument is computed or stored; its only job is to execute its own body using the values of the arguments passed to it.
any_name = 42
double(any_name)

The argument can also be any value that can be doubled. For example, a whole array of numbers can be passed as an argument to double, and the
result will be another array.
double(make_array(3, 4, 5))

array([ 6, 8, 10])

However, names that are defined inside a function, including arguments like double’s x, have only a fleeting existence. They are defined only while the
function is being called, and they are only accessible inside the body of the function. We can’t refer to x outside the body of double. The technical
terminology is that x has local scope.
Therefore the name x isn’t recognized outside the body of the function, even though we have called double in the cells above.
x

---------------------------------------------------------------------------
NameError Traceback (most recent call last)
<ipython-input-7-6fcf9dfbd479> in <module>
----> 1 x

NameError: name 'x' is not defined

Docstrings. Though double is relatively easy to understand, many functions perform complicated tasks and are difficult to use without explanation.
(You may have discovered this yourself!) Therefore, a well‑composed function has a name that evokes its behavior, as well as documentation. In
Python, this is called a docstring — a description of its behavior and expectations about its arguments. The docstring can also show example calls to
the function, where the call is preceded by >>>.
A docstring can be any string, as long as it is the first thing in a function’s body. Docstrings are typically defined using triple quotation marks at the
start and end, which allows a string to span multiple lines. The first line is conventionally a complete but short description of the function, while
following lines provide further guidance to future users of the function.
Here is a definition of a function called percent that takes two arguments. The definition includes a docstring.
# A function with more than one argument

def percent(x, total):

"""Convert x to a percentage of total.

More precisely, this function divides x by total,

multiplies the result by 100, and rounds the result
to two decimal places.

>>> percent(4, 16)

25.0
>>> percent(1, 6)
16.67
"""
return round((x/total)*100, 2)

percent(33, 200)

16.5

Contrast the function percent defined above with the function percents defined below. The latter takes an array as its argument, and converts all the
numbers in the array to percents out of the total of the values in the array. The percents are all rounded to two decimal places, this time replacing
round by np.round because the argument is an array and not a number.

def percents(counts):
"""Convert the values in array_x to percents out of the total of array_x."""
total = counts.sum()
return np.round((counts/total)*100, 2)

The function percents returns an array of percents that add up to 100 apart from rounding.
some_array = make_array(7, 10, 4)
percents(some_array)

array([33.33, 47.62, 19.05])

It is helpful to understand the steps Python takes to execute a function. To facilitate this, we have put a function definition and a call to that function
in the same cell below.
def biggest_difference(array_x):
"""Find the biggest difference in absolute value between two adjacent elements of
array_x."""
diffs = np.diff(array_x)
absolute_diffs = abs(diffs)
return max(absolute_diffs)

some_numbers = make_array(2, 4, 5, 6, 4, -1, 1)

big_diff = biggest_difference(some_numbers)
print("The biggest difference is", big_diff)

The biggest difference is 5

Here is what happens when we run that cell:

Multiple Arguments
There can be multiple ways to generalize an expression or block of code, and so a function can take multiple arguments that each determine different
aspects of the result. For example, the percents function we defined previously rounded to two decimal places every time. The following two‑
argument definition allows different calls to round to different amounts.
def percents(counts, decimal_places):
"""Convert the values in array_x to percents out of the total of array_x."""
total = counts.sum()
return np.round((counts/total)*100, decimal_places)

parts = make_array(2, 1, 4)
print("Rounded to 1 decimal place: ", percents(parts, 1))
print("Rounded to 2 decimal places:", percents(parts, 2))
print("Rounded to 3 decimal places:", percents(parts, 3))

Rounded to 1 decimal place: [28.6 14.3 57.1]

Rounded to 2 decimal places: [28.57 14.29 57.14]
Rounded to 3 decimal places: [28.571 14.286 57.143]
The flexibility of this new definition comes at a small price: each time the function is called, the number of decimal places must be specified. Default
argument values allow a function to be called with a variable number of arguments; any argument that isn’t specified in the call expression is given its
default value, which is stated in the first line of the def statement. For example, in this final definition of percents, the optional argument
decimal_places is given a default value of 2.

def percents(counts, decimal_places=2):

"""Convert the values in array_x to percents out of the total of array_x."""
total = counts.sum()
return np.round((counts/total)*100, decimal_places)

parts = make_array(2, 1, 4)
print("Rounded to 1 decimal place:", percents(parts, 1))
print("Rounded to the default number of decimal places:", percents(parts))

Rounded to 1 decimal place: [28.6 14.3 57.1]

Rounded to the default number of decimal places: [28.57 14.29 57.14]

Note: Methods
Functions are called by placing argument expressions in parentheses after the function name. Any function that is defined in isolation is called in this
way. You have also seen examples of methods, which are like functions but are called using dot notation, such as some_table.sort(some_label).
The functions that you define will always be called using the function name first, passing in all of the arguments.

8.1. Applying a Function to a Column

We have seen many examples of creating new columns of tables by applying functions to existing columns or to other arrays. All of those functions
took arrays as their arguments. But frequently we will want to convert the entries in a column by a function that doesn’t take an array as its argument.
For example, it might take just one number as its argument, as in the function cut_off_at_100 defined below.
def cut_off_at_100(x):
"""The smaller of x and 100"""
return min(x, 100)

cut_off_at_100(17)

cut_off_at_100(117)

100

cut_off_at_100(100)

100

The function cut_off_at_100 simply returns its argument if the argument is less than or equal to 100. But if the argument is greater than 100, it
returns 100.
In our earlier examples using Census data, we saw that the variable AGE had a value 100 that meant “100 years old or older”. Cutting off ages at 100 in
this manner is exactly what cut_off_at_100 does.
To use this function on many ages at once, we will have to be able to refer to the function itself, without actually calling it. Analogously, we might
show a cake recipe to a chef and ask her to use it to bake 6 cakes. In that scenario, we are not using the recipe to bake any cakes ourselves; our role
is merely to refer the chef to the recipe. Similarly, we can ask a table to call cut_off_at_100 on 6 different numbers in a column.
First, we create the table ages with a column for people and one for their ages. For example, person C is 52 years old.
ages = Table().with_columns(
'Person', make_array('A', 'B', 'C', 'D', 'E', 'F'),
'Age', make_array(17, 117, 52, 100, 6, 101)
)
ages

Person Age
A 17
B 117
C 52
D 100
E 6
F 101

8.1.1. apply
To cut off each of the ages at 100, we will use a new Table method. The apply method calls a function on each element of a column, forming a new
array of return values. To indicate which function to call, just name it (without quotation marks or parentheses). The name of the column of input
values is a string that must still appear within quotation marks.
ages.apply(cut_off_at_100, 'Age')

array([ 17, 100, 52, 100, 6, 100])

What we have done here is apply the function cut_off_at_100 to each value in the Age column of the table ages. The output is the array of
corresponding return values of the function. For example, 17 stayed 17, 117 became 100, 52 stayed 52, and so on.
This array, which has the same length as the original Age column of the ages table, can be used as the values in a new column called Cut Off Age
alongside the existing Person and Age columns.
ages.with_column(
'Cut Off Age', ages.apply(cut_off_at_100, 'Age')
)

Person Age Cut Off Age

A 17 17
B 117 100
C 52 52
D 100 100
E 6 6
F 101 100

8.1.2. Functions as Values

We’ve seen that Python has many kinds of values. For example, 6 is a number value, "cake" is a text value, Table() is an empty table, and ages is a
name for a table value (since we defined it above).
In Python, every function, including cut_off_at_100, is also a value. It helps to think about recipes again. A recipe for cake is a real thing, distinct
from cakes or ingredients, and you can give it a name like “Ani’s cake recipe.” When we defined cut_off_at_100 with a def statement, we actually did
two separate things: we created a function that cuts off numbers at 100, and we gave it the name cut_off_at_100.
We can refer to any function by writing its name, without the parentheses or arguments necessary to actually call it. We did this when we called apply
above. When we write a function’s name by itself as the last line in a cell, Python produces a text representation of the function, just like it would print
out a number or a string value.
cut_off_at_100

Notice that we did not write "cut_off_at_100" with quotes (which is just a piece of text), or cut_off_at_100() (which is a function call, and an
invalid one at that). We simply wrote cut_off_at_100 to refer to the function.
Just like we can define new names for other values, we can define new names for functions. For example, suppose we want to refer to our function as
cut_off instead of cut_off_at_100. We can just write this:

cut_off = cut_off_at_100

Now cut_off is a name for a function. It’s the same function as cut_off_at_100, so the printed value is exactly the same.
cut_off

Let us see another application of apply.

8.1.3. Example: Prediction

Data science is often used to make predictions about the future. If we are trying to predict an outcome for a particular individual – for example, how
she will respond to a treatment, or whether he will buy a product – it is natural to base the prediction on the outcomes of other similar individuals.
The table below is adapted from a historical data set on the heights of parents and their adult children. Each row corresponds to one adult child. The
variables are a numerical code for the family, the heights (in inches) of the father and mother, the number of children in the family, as well as the
child’s birth rank (1 = oldest), sex (coded only as “male” or “female”), and height in inches.
# Data on heights of parents and their adult children
family_heights = Table.read_table(path_data + 'family_heights.csv').drop(3)
family_heights

family father mother children childNum sex childHeight

1 78.5 67 4 1 male 73.2
1 78.5 67 4 2 female 69.2
1 78.5 67 4 3 female 69
1 78.5 67 4 4 female 69
2 75.5 66.5 4 1 male 73.5
2 75.5 66.5 4 2 male 72.5
2 75.5 66.5 4 3 female 65.5
2 75.5 66.5 4 4 female 65.5
3 75 64 2 1 male 71
3 75 64 2 2 female 68
... (924 rows omitted)
A primary reason for collecting the data was to be able to predict the adult height of a child born to parents similar to those in the dataset. Let us try
to do this, by using the simple average of the parents’ height as the variable on which to base our prediction.
This parent average height is our predictor variable. In the cell below, its values are in the array parent_averages.
The table heights consists of just the parent average heights and child heights. The scatter plot of the two variables shows a positive association as
we would expect for these variables.
parent_averages = (family_heights.column('father') + family_heights.column('mother'))/2
heights = Table().with_columns(
'Parent Average', parent_averages,
'Child', family_heights.column('childHeight')
)
heights

Parent Average Child

72.75 73.2
72.75 69.2
72.75 69
72.75 69
71 73.5
71 72.5
71 65.5
71 65.5
69.5 71
69.5 68
... (924 rows omitted)
heights.scatter('Parent Average')

Now suppose the researchers encountered a new couple, similar to those in this dataset, and wondered how tall their child would be. What would be
a good way for him to go about predicting the child’s height, given that the parent average height was, say, 68 inches?
One reasonable approach would be to base the prediction on all the points that correspond to a parent average height of around 68 inches. The
prediction equals the average child’s height calculated from those points alone.
Let’s execute this plan. For now we will just make a reasonable definition of what “around 68 inches” means, and work with that. Later in the course
we will examine the consequences of such choices.
We will take “close” to mean “within half an inch”. The figure below shows all the points corresponding to a parent average height between 67.5
inches and 68.5 inches. These are all the points in the strip between the red lines. Each of these points corresponds to one child; our prediction of
the height of the new couple’s child is the average height of all the children in the strip. That’s represented by the gold dot.
Ignore the code, and just focus on understanding the mental process of arriving at that gold dot.
heights.scatter('Parent Average')
plots.plot([67.5, 67.5], [50, 85], color='red', lw=2)
plots.plot([68.5, 68.5], [50, 85], color='red', lw=2)
plots.scatter(68, 67.62, color='gold', s=40);
In order to calculate exactly where the gold dot should be, we first need to indentify all the points in the strip. These correspond to the rows where
Parent Average is between 67.5 inches and 68.5 inches.

close_to_68 = heights.where('Parent Average', are.between(67.5, 68.5))

close_to_68

Parent Average Child

68 74
68 70
68 68
68 67
68 67
68 66
68 63.5
68 63
67.5 65
68.1 62.7
... (175 rows omitted)
The predicted height of a child who has a parent average height of 68 inches is the average height of the children in these rows. That’s 67.62 inches.
np.average(close_to_68.column('Child'))

67.62

We now have a way to predict the height of a child given any value of the parent average height near those in our dataset. We can define a function
predict_child that does this. The body of the function consists of the code in the two cells above, apart from choices of names.

def predict_child(p_avg):
"""Predict the height of a child whose parents have a parent average height of
p_avg.

The prediction is the average height of the children whose parent average height is
in the range p_avg plus or minus 0.5.
"""

close_points = heights.where('Parent Average', are.between(p_avg-0.5, p_avg + 0.5))

return np.average(close_points.column('Child'))

Given a parent average height of 68 inches, the function predict_child returns the same prediction (67.62 inches) as we got earlier. The advantage
of defining the function is that we can easily change the value of the predictor and get a new prediction.
predict_child(68)
67.62

predict_child(66)

66.08640776699029

How good are these predictions? We can get a sense of this by comparing the predictions with the data that we already have. To do this, we first
apply the function predict_child to the column of Parent Average heights, and collect the results in a new column labeled Prediction.
# Apply predict_child to all the midparent heights

heights_with_predictions = heights.with_column(
'Prediction', heights.apply(predict_child, 'Parent Average')
)

heights_with_predictions

Parent Average Child Prediction

72.75 73.2 70.1
72.75 69.2 70.1
72.75 69 70.1
72.75 69 70.1
71 73.5 70.4158
71 72.5 70.4158
71 65.5 70.4158
71 65.5 70.4158
69.5 71 68.5025
69.5 68 68.5025
... (924 rows omitted)
To see where the predictions lie relative to the observed data, we can draw overlaid scatter plots with Parent Average as the common horizontal axis.
heights_with_predictions.scatter('Parent Average')

The graph of gold dots is called a graph of averages, because each gold dot is the center of a vertical strip like the one we drew earlier. Each one
provides a prediction of a child’s height given the parent average height. For example, the scatter shows that for a parent average height of 65
inches, the predicted height of the child would be just above 65 inches, and indeed predict_child(65) evaluates to about 65.84.
predict_child(65)

65.83829787234043
Notice that the graph of averages roughly follows a straight line. This straight line is now called the regression line and is one of the most common
methods of making predictions. The calculation that we have just done is very similar to the calculation that led to the development of the regression
method, using the same data.
This example, like the one about John Snow’s analysis of cholera deaths, shows how some of the fundamental concepts of modern data science have
roots going back a long way. The method used here was a precursor to nearest neighbor prediction methods that now have powerful applications in
diverse settings. The modern field of machine learning includes the automation of such methods to make predictions based on vast and rapidly
evolving datasets.

8.2. Classifying by One Variable

Data scientists often need to classify individuals into groups according to shared features, and then identify some characteristics of the groups. For
example, in the example using Galton’s data on heights, we saw that it was useful to classify families according to the parents’ midparent heights, and
then find the average height of the children in each group.
This section is about classifying individuals into categories that are not numerical. We begin by recalling the basic use of group.

8.2.1. Counting the Number in Each Category

The group method with a single argument counts the number of rows for each category in a column. The result contains one row per unique value in
the grouped column.
Here is a small table of data on ice cream cones. The group method can be used to list the distinct flavors and provide the counts of each flavor.
cones = Table().with_columns(
'Flavor', make_array('strawberry', 'chocolate', 'chocolate', 'strawberry',
'chocolate'),
'Price', make_array(3.55, 4.75, 6.55, 5.25, 5.25)
)
cones

Flavor Price
strawberry 3.55
chocolate 4.75
chocolate 6.55
strawberry 5.25
chocolate 5.25
cones.group('Flavor')

Flavor count
chocolate 3
strawberry 2
There are two distinct categories, chocolate and strawberry. The call to group creates a table of counts in each category. The column is called count
by default, and contains the number of rows in each category.
Notice that this can all be worked out from just the Flavor column. The Price column has not been used.
But what if we wanted the total price of the cones of each different flavor? That’s where the second argument of group comes in.

8.2.2. Finding a Characteristic of Each Category

The optional second argument of group names the function that will be used to aggregate values in other columns for all of those rows. For instance,
sum will sum up the prices in all rows that match each category. This result also contains one row per unique value in the grouped column, but it has
the same number of columns as the original table.
To find the total price of each flavor, we call group again, with Flavor as its first argument as before. But this time there is a second argument: the
function name sum.
cones.group('Flavor', sum)

Flavor Price sum

chocolate 16.55
strawberry 8.8
To create this new table, group has calculated the sum of the Price entries in all the rows corresponding to each distinct flavor. The prices in the
three chocolate rows add up to $\$16.55$ (you can assume that price is being measured in dollars). The prices in the two strawberry rows have a
total of $\$8.80$.
The label of the newly created “sum” column is Price sum, which is created by taking the label of the column being summed, and appending the
word sum.
Because group finds the sum of all columns other than the one with the categories, there is no need to specify that it has to sum the prices.
To see in more detail what group is doing, notice that you could have figured out the total prices yourself, not only by mental arithmetic but also using
code. For example, to find the total price of all the chocolate cones, you could start by creating a new table consisting of only the chocolate cones,
and then accessing the column of prices:
cones.where('Flavor', are.equal_to('chocolate')).column('Price')

array([4.75, 6.55, 5.25])

sum(cones.where('Flavor', are.equal_to('chocolate')).column('Price'))

16.55

This is what group is doing for each distinct value in Flavor.

# For each distinct value in `Flavor, access all the rows
# and create an array of `Price`

cones_choc = cones.where('Flavor', are.equal_to('chocolate')).column('Price')

cones_strawb = cones.where('Flavor', are.equal_to('strawberry')).column('Price')

# Display the arrays in a table

grouped_cones = Table().with_columns(
'Flavor', make_array('chocolate', 'strawberry'),
'Array of All the Prices', make_array(cones_choc, cones_strawb)
)

# Append a column with the sum of the `Price` values in each array

price_totals = grouped_cones.with_column(
'Sum of the Array', make_array(sum(cones_choc), sum(cones_strawb))
)
price_totals

Flavor Array of All the Prices Sum of the Array

chocolate [4.75 6.55 5.25] 16.55
strawberry [3.55 5.25] 8.8
You can replace sum by any other functions that work on arrays. For example, you could use max to find the largest price in each category:
cones.group('Flavor', max)
Flavor Price max
chocolate 6.55
strawberry 5.25
Once again, group creates arrays of the prices in each Flavor category. But now it finds the max of each array:
price_maxes = grouped_cones.with_column(
'Max of the Array', make_array(max(cones_choc), max(cones_strawb))
)
price_maxes

Flavor Array of All the Prices Max of the Array

chocolate [4.75 6.55 5.25] 6.55
strawberry [3.55 5.25] 5.25
Indeed, the original call to group with just one argument has the same effect as using len as the function and then cleaning up the table.
lengths = grouped_cones.with_column(
'Length of the Array', make_array(len(cones_choc), len(cones_strawb))
)
lengths

Flavor Array of All the Prices Length of the Array

chocolate [4.75 6.55 5.25] 3
strawberry [3.55 5.25] 2

8.2.3. Example: NBA Salaries

The table nba contains data on the 2015‑2016 players in the National Basketball Association. We have examined these data earlier. Recall that salaries
are measured in millions of dollars.
nba1 = Table.read_table(path_data + 'nba_salaries.csv')
nba = nba1.relabeled("'15-'16 SALARY", 'SALARY')
nba

PLAYER POSITION TEAM SALARY

Paul Millsap PF Atlanta Hawks 18.6717
Al Horford C Atlanta Hawks 12
Tiago Splitter C Atlanta Hawks 9.75625
Jeff Teague PG Atlanta Hawks 8
Kyle Korver SG Atlanta Hawks 5.74648
Thabo Sefolosha SF Atlanta Hawks 4
Mike Scott PF Atlanta Hawks 3.33333
Kent Bazemore SF Atlanta Hawks 2
Dennis Schroder PG Atlanta Hawks 1.7634
Tim Hardaway Jr. SG Atlanta Hawks 1.30452
... (407 rows omitted)
1. How much money did each team pay for its players’ salaries?
The only columns involved are TEAM and SALARY. We have to group the rows by TEAM and then sum the salaries of the groups.
teams_and_money = nba.select('TEAM', 'SALARY')
teams_and_money.group('TEAM', sum)
TEAM SALARY sum
Atlanta Hawks 69.5731
Boston Celtics 50.2855
Brooklyn Nets 57.307
Charlotte Hornets 84.1024
Chicago Bulls 78.8209
Cleveland Cavaliers 102.312
Dallas Mavericks 65.7626
Denver Nuggets 62.4294
Detroit Pistons 42.2118
Golden State Warriors 94.0851
... (20 rows omitted)
2. How many NBA players were there in each of the five positions?
We have to classify by POSITION, and count. This can be done with just one argument to group:
nba.group('POSITION')

POSITION count
C 69
PF 85
PG 85
SF 82
SG 96
3. What was the average salary of the players at each of the five positions?
This time, we have to group by POSITION and take the mean of the salaries. For clarity, we will work with a table of just the positions and the salaries.
positions_and_money = nba.select('POSITION', 'SALARY')
positions_and_money.group('POSITION', np.mean)

POSITION SALARY mean

C 6.08291
PF 4.95134
PG 5.16549
SF 5.53267
SG 3.9882
Center was the most highly paid position, at an average of over 6 million dollars.
If we had not selected the two columns as our first step, group would not attempt to “average” the categorical columns in nba. (It is impossible to
average two strings like “Atlanta Hawks” and “Boston Celtics”.) It performs arithmetic only on numerical columns and leaves the rest blank.
nba.group('POSITION', np.mean)
POSITION PLAYER mean TEAM mean SALARY mean
C 6.08291
PF 4.95134
PG 5.16549
SF 5.53267
SG 3.9882

8.3. Cross‑Classifying by More than One Variable

When individuals have multiple features, there are many different ways to classify them. For example, if we have a population of college students for
each of whom we have recorded a major and the number of years in college, then the students could be classified by major, or by year, or by a
combination of major and year.
The group method also allows us to classify individuals according to multiple variables. This is called cross‑classifying.

8.3.1. Two Variables: Counting the Number in Each Paired Category

The table more_cones records the flavor, color, and price of six ice cream cones.
more_cones = Table().with_columns(
'Flavor', make_array('strawberry', 'chocolate', 'chocolate', 'strawberry',
'chocolate', 'bubblegum'),
'Color', make_array('pink', 'light brown', 'dark brown', 'pink', 'dark brown',
'pink'),
'Price', make_array(3.55, 4.75, 5.25, 5.25, 5.25, 4.75)
)

more_cones

Flavor Color Price

strawberry pink 3.55
chocolate light brown 4.75
chocolate dark brown 5.25
strawberry pink 5.25
chocolate dark brown 5.25
bubblegum pink 4.75
We know how to use group to count the number of cones of each flavor:
more_cones.group('Flavor')

Flavor count
bubblegum 1
chocolate 3
strawberry 2
But now each cone has a color as well. To classify the cones by both flavor and color, we will pass a list of labels as an argument to group. The
resulting table has one row for every unique combination of values that appear together in the grouped columns. As before, a single argument (a list,
in this case, but an array would work too) gives row counts.
Although there are six cones, there are only four unique combinations of flavor and color. Two of the cones were dark brown chocolate, and two pink
strawberry.
more_cones.group(['Flavor', 'Color'])
Flavor Color count
bubblegum pink 1
chocolate dark brown 2
chocolate light brown 1
strawberry pink 2

8.3.2. Two Variables: Finding a Characteristic of Each Paired Category

A second argument aggregates all other columns that are not in the list of grouped columns.
more_cones.group(['Flavor', 'Color'], sum)

Flavor Color Price sum

bubblegum pink 4.75
chocolate dark brown 10.5
chocolate light brown 4.75
strawberry pink 8.8
Three or More Variables. You can use group to classify rows by three or more categorical variables. Just include them all in the list that is the first
argument. But cross‑classifying by multiple variables can become complex, as the number of distinct combinations of categories can be quite large.

8.3.3. Pivot Tables: Rearranging the Output of group

Many uses of cross‑classification involve just two categorical variables, like Flavor and Color in the example above. In these cases it is possible to
display the results of the classification in a different kind of table, called a pivot table. Pivot tables, also known as contingency tables, make it easier
to work with data that have been classified according to two variables.
Recall the use of group to count the number of cones in each paired category of flavor and color:
more_cones.group(['Flavor', 'Color'])

Flavor Color count

bubblegum pink 1
chocolate dark brown 2
chocolate light brown 1
strawberry pink 2
The same data can be displayed differenly using the Table method pivot. Ignore the code for a moment, and just examine the table of outcomes.
more_cones.pivot('Flavor', 'Color')

Color bubblegum chocolate strawberry

dark brown 0 2 0
light brown 0 1 0
pink 1 0 2
Notice how this table displays all nine possible pairs of flavor and color, including pairs like “dark brown bubblegum” that don’t exist in our data.
Notice also that the count in each pair appears in the body of the table: to find the number of light brown chocolate cones, run your eye along the row
light brown until it meets the column chocolate.

The group method takes a list of two labels because it is flexible: it could take one or three or more. On the other hand, pivot always takes two
column labels, one to determine the columns and one to determine the rows.
pivot

The pivot method is closely related to the group method: it groups together rows that share a combination of values. It differs from group because it
organizes the resulting values in a grid. The first argument to pivot is the label of a column that contains the values that will be used to form new
columns in the result. The second argument is the label of a column used for the rows. The result gives the count of all rows of the original table that
share the combination of column and row values.
Like group, pivot can be used with additional arguments to find characteristics of each paired category. An optional third argument called values
indicates a column of values that will replace the counts in each cell of the grid. All of these values will not be displayed, however; the fourth
argument collect indicates how to collect them all into one aggregated value to be displayed in the cell.
An example will help clarify this. Here is pivot being used to find the total price of the cones in each cell.
more_cones.pivot('Flavor', 'Color', values='Price', collect=sum)

Color bubblegum chocolate strawberry

dark brown 0 10.5 0
light brown 0 4.75 0
pink 4.75 0 8.8
And here is group doing the same thing.
more_cones.group(['Flavor', 'Color'], sum)

Flavor Color Price sum

bubblegum pink 4.75
chocolate dark brown 10.5
chocolate light brown 4.75
strawberry pink 8.8
Though the numbers in both tables are the same, table produced by pivot is easier to read and lends itself more easily to analysis. The advantage of
pivot is that it places grouped values into adjacent columns, so that they can be combined and compared.

8.3.4. Example: Education and Income of Californian Adults

The State of California’s Open Data Portal is a rich source of information about the lives of Californians. It is our source of a dataset on educational
attainment and personal income among Californians over the years 2008 to 2014. The data are derived from the U.S. Census Current Population
Survey.
For each year, the table records the Population Count of Californians in many different combinations of age, gender, educational attainment, and
personal income. We will study only the data for the year 2014.
full_table = Table.read_table(path_data + 'educ_inc.csv')
ca_2014 = full_table.where('Year', are.equal_to('1/1/14 0:00')).where('Age',
are.not_equal_to('00 to 17'))
ca_2014
Year Age Gender Educational Attainment Personal Population
Income Count
1/1/14 18 to 64 Female No high school diploma H: 75,000 and 2058
0 00 over
1/1/14 65 to Male No high school diploma H: 75,000 and 2153
0 00 80+ over
1/1/14 65 to Female No high school diploma G: 50,000 to 4666
0 00 80+ 74,999
1/1/14 65 to Female High school or equivalent H: 75,000 and 7122
0 00 80+ over
1/1/14 65 to Female No high school diploma F: 35,000 to 7261
0 00 80+ 49,999
1/1/14 65 to Male No high school diploma G: 50,000 to 8569
0 00 80+ 74,999
1/1/14 18 to 64 Female No high school diploma G: 50,000 to 14635
0 00 74,999
1/1/14 65 to Male No high school diploma F: 35,000 to 15212
0 00 80+ 49,999
1/1/14 65 to Male College, less than 4‑yr B: 5,000 to 9,999 15423
0 00 80+ degree
1/1/14 65 to Female Bachelor's degree or A: 0 to 4,999 15459
0 00 80+ higher
... (117 rows omitted)
Each row of the table corresponds to a combination of age, gender, educational level, and income. There are 127 such combinations in all!
As a first step it is a good idea to start with just one or two variables. We will focus on just one pair: educational attainment and personal income.
educ_inc = ca_2014.select('Educational Attainment', 'Personal Income', 'Population
Count')
educ_inc

Educational Attainment Personal Income Population Count

No high school diploma H: 75,000 and over 2058
No high school diploma H: 75,000 and over 2153
No high school diploma G: 50,000 to 74,999 4666
High school or equivalent H: 75,000 and over 7122
No high school diploma F: 35,000 to 49,999 7261
No high school diploma G: 50,000 to 74,999 8569
No high school diploma G: 50,000 to 74,999 14635
No high school diploma F: 35,000 to 49,999 15212
College, less than 4‑yr degree B: 5,000 to 9,999 15423
Bachelor's degree or higher A: 0 to 4,999 15459
... (117 rows omitted)
Let’s start by looking at educational level alone. The categories of this variable have been subdivided by the different levels of income. So we will
group the table by Educational Attainment and sum the Population Count in each category.
education = educ_inc.select('Educational Attainment', 'Population Count')
educ_totals = education.group('Educational Attainment', sum)
educ_totals
Educational Attainment Population Count sum
Bachelor's degree or higher 8525698
College, less than 4‑yr degree 7775497
High school or equivalent 6294141
No high school diploma 4258277
There are only four categories of educational attainment. The counts are so large that is is more helpful to look at percents. For this, we will use the
function percents that we defined in an earlier section. It converts an array of numbers to an array of percents out of the total in the input array.
def percents(array_x):
return np.round( (array_x/sum(array_x))*100, 2)

We now have the distribution of educational attainment among adult Californians. More than 30% have a Bachelor’s degree or higher, while almost
16% lack a high school diploma.
educ_distribution = educ_totals.with_column(
'Population Percent', percents(educ_totals.column(1))
)
educ_distribution

Educational Attainment Population Count sum Population Percent

Bachelor's degree or higher 8525698 31.75
College, less than 4‑yr degree 7775497 28.96
High school or equivalent 6294141 23.44
No high school diploma 4258277 15.86
By using pivot, we can get a contingency table (a table of counts) of adult Californians cross‑classified by Educational Attainment and Personal
Income.

totals = educ_inc.pivot('Educational Attainment', 'Personal Income', values='Population

Count', collect=sum)
totals

Personal Bachelor's degree College, less than High school or No high school
Income or higher 4‑yr degree equivalent diploma
A: 0 to 575491 985011 1161873 1204529
4,999
B: 5,000 to 326020 810641 626499 597039
9,999
C: 10,000 to 452449 798596 692661 664607
14,999
D: 15,000 to 773684 1345257 1252377 875498
24,999
E: 25,000 to 693884 1091642 929218 464564
34,999
F: 35,000 to 1122791 1112421 782804 260579
49,999
G: 50,000 to 1594681 883826 525517 132516
74,999
H: 75,000 2986698 748103 323192 58945
and over
Here you see the power of pivot over other cross‑classification methods. Each column of counts is a distribution of personal income at a specific
level of educational attainment. Converting the counts to percents allows us to compare the four distributions.
distributions = totals.select(0).with_columns(
"Bachelor's degree or higher", percents(totals.column(1)),
'College, less than 4-yr degree', percents(totals.column(2)),
'High school or equivalent', percents(totals.column(3)),
'No high school diploma', percents(totals.column(4))
)

distributions

Personal Bachelor's degree College, less than High school or No high school
Income or higher 4‑yr degree equivalent diploma
A: 0 to 6.75 12.67 18.46 28.29
4,999
B: 5,000 to 3.82 10.43 9.95 14.02
9,999
C: 10,000 to 5.31 10.27 11 15.61
14,999
D: 15,000 to 9.07 17.3 19.9 20.56
24,999
E: 25,000 to 8.14 14.04 14.76 10.91
34,999
F: 35,000 to 13.17 14.31 12.44 6.12
49,999
G: 50,000 to 18.7 11.37 8.35 3.11
74,999
H: 75,000 35.03 9.62 5.13 1.38
and over
At a glance, you can see that over 35% of those with Bachelor’s degrees or higher had incomes of $\$75,000$ and over, whereas fewer than 10% of
the people in the other education categories had that level of income.
The bar chart below compares the personal income distributions of adult Californians who have no high school diploma with those who have
completed a Bachelor’s degree or higher. The difference in the distributions is striking. There is a clear positive association between educational
attainment and personal income.
distributions.select(0, 1, 4).barh(0)

8.4. Joining Tables by Columns

Often, data about the same individuals is maintained in more than one table. For example, one university office might have data about each student’s
time to completion of degree, while another has data about the student’s tuition and financial aid.
To understand the students’ experience, it may be helpful to put the two datasets together. If the data are in two tables, each with one row per
student, then we would want to put the columns together, making sure to match the rows so that each student’s information remains on a single row.
Let us do this in the context of a simple example, and then use the method with a larger dataset.
The table cones is one we have encountered earlier. Now suppose each flavor of ice cream comes with a rating that is in a separate table.
cones = Table().with_columns(
'Flavor', make_array('strawberry', 'vanilla', 'chocolate', 'strawberry',
'chocolate'),
'Price', make_array(3.55, 4.75, 6.55, 5.25, 5.75)
)
cones

Flavor Price
strawberry 3.55
vanilla 4.75
chocolate 6.55
strawberry 5.25
chocolate 5.75
ratings = Table().with_columns(
'Kind', make_array('strawberry', 'chocolate', 'vanilla'),
'Stars', make_array(2.5, 3.5, 4)
)
ratings

Kind Stars
strawberry 2.5
chocolate 3.5
vanilla 4
Each of the tables has a column that contains ice cream flavors: cones has the column Flavor, and ratings has the column Kind. The entries in these
columns can be used to link the two tables.
The method join creates a new table in which each cone in the cones table is augmented with the Stars information in the ratings table. For each
cone in cones, join finds a row in ratings whose Kind matches the cone’s Flavor. We have to tell join to use those columns for matching.
rated = cones.join('Flavor', ratings, 'Kind')
rated

Flavor Price Stars

chocolate 6.55 3.5
chocolate 5.75 3.5
strawberry 3.55 2.5
strawberry 5.25 2.5
vanilla 4.75 4
Each cone now has not only its price but also the rating of its flavor.
In general, a call to join that augments a table (say table1) with information from another table (say table2) looks like this:
table1.join(table1_column_for_joining, table2, table2_column_for_joining)

The new table rated allows us to work out the price per star, which you can think of as an informal measure of value. Low values are good – they
mean that you are paying less for each rating star.
rated.with_column('$/Star', rated.column('Price') / rated.column('Stars')).sort(3)
Flavor Price Stars $/Star
vanilla 4.75 4 1.1875
strawberry 3.55 2.5 1.42
chocolate 5.75 3.5 1.64286
chocolate 6.55 3.5 1.87143
strawberry 5.25 2.5 2.1
Though strawberry has the lowest rating among the three flavors, the less expensive strawberry cone does well on this measure because it doesn’t
cost a lot per star.
Side note. Does the order we list the two tables matter? Let’s try it. As you see it, this changes the order that the columns appear in, and can
potentially changes the order of the rows, but it doesn’t make any fundamental difference.
ratings.join('Kind', cones, 'Flavor')

Kind Stars Price

chocolate 3.5 6.55
chocolate 3.5 5.75
strawberry 2.5 3.55
strawberry 2.5 5.25
vanilla 4 4.75
Also note that the join will only contain information about items that appear in both tables. Let’s see an example. Suppose there is a table of reviews
of some ice cream cones, and we have found the average review for each flavor.
reviews = Table().with_columns(
'Flavor', make_array('vanilla', 'chocolate', 'vanilla', 'chocolate'),
'Stars', make_array(5, 3, 5, 4)
)
reviews

Flavor Stars
vanilla 5
chocolate 3
vanilla 5
chocolate 4
average_review = reviews.group('Flavor', np.average)
average_review

Flavor Stars average

chocolate 3.5
vanilla 5
We can join cones and average_review by providing the labels of the columns by which to join.
cones.join('Flavor', average_review, 'Flavor')

Flavor Price Stars average

chocolate 6.55 3.5
chocolate 5.75 3.5
vanilla 4.75 5
Notice how the strawberry cones have disappeared. None of the reviews are for strawberry cones, so there is nothing to which the strawberry rows
can be joined. This might be a problem, or it might not be ‑ that depends on the analysis we are trying to perform with the joined table.

8.5. Bike Sharing in the Bay Area

We end this chapter by using all the methods we have learned to examine a new and large dataset. We will also introduce map_table, a powerful
visualization tool.
The Bay Area Bike Share service published a dataset describing every bicycle rental from September 2014 to August 2015 in their system. There were
354,152 rentals in all. The columns are:
An ID for the rental
Duration of the rental, in seconds
Start date
Name of the Start Station and code for Start Terminal
Name of the End Station and code for End Terminal
A serial number for the bike
Subscriber type and zip code
trips = Table.read_table(path_data + 'trip.csv')
trips

Trip ID Duration Start Start Start End

Date Station Terminal End Date End Station Terminal
Harry San
Francisco
913460 765 8/31/2015
23 26
Bridges
Plaza (Ferry
8/31/2015
50 23 39 Caltrain 70
Building) (Townsend
at 4th)
San Antonio Mountain
913459 1036 8/31/2015
23 11 Shopping 31 8/31/2015
23 28 View City 27
Center Hall
913455 307 8/31/2015
23 13
Post at
Kearny 47 8/31/2015
23 18
2nd at South
Park 64
913454 409 8/31/2015
23 10
San Jose
City Hall 10 8/31/2015
23 17
San Salvador
at 1st 8
913453 789 8/31/2015
23 09
Embarcadero
at Folsom 51 8/31/2015 Embarcadero
23 22 at Sansome 60
Yerba Buena San
Francisco
913452 293 8/31/2015
23 07
Center of the
Arts (3rd @ 68 8/31/2015 Caltrain
23 12 (Townsend 70
Howard) at 4th)
913451 896 8/31/2015
23 07
Embarcadero
at Folsom 51 8/31/2015 Embarcadero
23 22 at Sansome 60
913450 255 8/31/2015
22 16
Embarcadero
at Sansome 60 8/31/2015
22 20
Steuart at
Market 74
Temporary
Transbay
913449 126 8/31/2015
22 12
Beale at
Market 56 8/31/2015 Terminal
22 15 (Howard 55
at
Beale)
South Van
913448 932 8/31/2015
21 57
Post at
Kearny 47 8/31/2015
22 12 Ness at 66
Market
... (354142 rows omitted)
We’ll focus only on the free trips, which are trips that last less than 1800 seconds (half an hour). There is a charge for longer trips.
The histogram below shows that most of the trips took around 10 minutes (600 seconds) or so. Very few took near 30 minutes (1800 seconds),
possibly because people try to return the bikes before the cutoff time so as not to have to pay.
commute = trips.where('Duration', are.below(1800))
commute.hist('Duration', unit='Second')

We can get more detail by specifying a larger number of bins. But the overall shape doesn’t change much.
commute.hist('Duration', bins=60, unit='Second')

8.5.1. Exploring the Data with group and pivot

We can use group to identify the most highly used Start Station:
starts = commute.group('Start Station').sort('count', descending=True)
starts

Start Station count

Start Station End Station count

2nd at Folsom 2nd at Folsom 54
2nd at Folsom 2nd at South Park 295
2nd at Folsom 2nd at Townsend 437
2nd at Folsom 5th at Howard 113
2nd at Folsom Beale at Market 127
2nd at Folsom Broadway St at Battery St 67
2nd at Folsom Civic Center BART (7th at Market) 47
2nd at Folsom Clay at Battery 240
2nd at Folsom Commercial at Montgomery 128
2nd at Folsom Davis at Jackson 28
... (1619 rows omitted)
Fifty‑four trips both started and ended at the station on 2nd at Folsom. A much large number (437) were between 2nd at Folsom and 2nd at
Townsend.
The pivot method does the same classification but displays its results in a contingency table that shows all possible combinations of Start and End
Stations, even though some of them didn’t correspond to any trips. Remember that the first argument of a pivot statement specifies the column
labels of the pivot table; the second argument labels the rows.
There is a train station as well as a Bay Area Rapid Transit (BART) station near Beale at Market, explaining the high number of trips that start and end
there.
commute.pivot('Start Station', 'End Station')
2nd Arena Beale Broadway
End 2nd at at 2nd at 5th at Adobe Green
on / SAP St at
at Battery
Station Folsom South Townsend Howard Almaden Market
Park Center St
2nd at 54 190 554 107 0 0 40 21
Folsom
2nd at
South 295 164 71 180 0 0 208 85
Park
2nd at
Townsend 437 151 185 92 0 0 608 350
5th at 113 177 148 83 0 0 59 130
Howard
Adobe on 0 0 0 0 11 4 0 0
Almaden
Arena
Green / 0 0 0 0 7 64 0 0
SAP
Center
Beale at 127 79 183 59 0 0 59 661
Market
Broadway
St at 67 89 279 119 0 0 1022 110
Battery St
California
Ave 0 0 0 0 0 0 0 0
Caltrain
Station
Castro
Street
and El 0 0 0 0 0 0 0 0
Camino
Real
... (60 rows omitted)
We can also use pivot to find the shortest time of the rides between Start and End Stations. Here pivot has been given Duration as the optional
values argument, and min as the function which to perform on the values in each cell.

commute.pivot('Start Station', 'End Station', 'Duration', min)

2nd Arena Beale Broadway
End 2nd at at 2nd at 5th at Adobe Green
on / SAP St at
at Battery
Station Folsom South Townsend Howard Almaden Market
Park Center St
2nd at 61 97 164 268 0 0 271 407
Folsom
2nd at
South 61 60 77 86 0 0 78 345
Park
2nd at
Townsend 137 67 60 423 0 0 311 469
5th at
Howard 215 300 384 68 0 0 357 530
Adobe on 0 0 0 0 84 275 0 0
Almaden
Arena
Green / 0 0 0 0 305 62 0 0
SAP
Center
Beale at 219 343 417 387 0 0 60 155
Market
Broadway
St at 351 424 499 555 0 0 195 62
Battery St
California
Ave 0 0 0 0 0 0 0 0
Caltrain
Station
Castro
Street
and El 0 0 0 0 0 0 0 0
Camino
Real
... (60 rows omitted)
Someone had a very quick trip (271 seconds, or about 4.5 minutes) from 2nd at Folsom to Beale at Market, about five blocks away. There are no bike
trips between the 2nd Avenue stations and Adobe on Almaden, because the latter is in a different city.

8.5.2. Drawing Maps

The table stations contains geographical information about each bike station, including latitude, longitude, and a “landmark” which is the name of
the city where the station is located.
stations = Table.read_table(path_data + 'station.csv')
stations
station_id name lat long dockcount landmark installation
2 San Jose Diridon 37.3297 ‑121.902 27 San Jose 8/6/2013
Caltrain Station
3 San Jose Civic Center 37.3307 ‑121.889 15 San Jose 8/5/2013
4 Santa Clara at 37.334 ‑121.895 11 San Jose 8/6/2013
Almaden
5 Adobe on Almaden 37.3314 ‑121.893 19 San Jose 8/5/2013
6 San Pedro Square 37.3367 ‑121.894 15 San Jose 8/7/2013
7 Paseo de San Antonio 37.3338 ‑121.887 15 San Jose 8/7/2013
8 San Salvador at 1st 37.3302 ‑121.886 15 San Jose 8/5/2013
9 Japantown 37.3487 ‑121.895 15 San Jose 8/5/2013
10 San Jose City Hall 37.3374 ‑121.887 15 San Jose 8/6/2013
11 MLK Library 37.3359 ‑121.886 19 San Jose 8/6/2013
... (60 rows omitted)
We can draw a map of where the stations are located, using Marker.map_table. The function operates on a table, whose columns are (in order)
latitude, longitude, and an optional identifier for each point.
Marker.map_table(stations.select('lat', 'long', 'name').relabel('name', 'labels'))

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The map is created using OpenStreetMap, which is an open online mapping system that you can use just as you would use Google Maps or any other
online map. Zoom in to San Francisco to see how the stations are distributed. Click on a marker to see which station it is.
You can also represent points on a map by colored circles. Here is such a map of the San Francisco bike stations.
sf = stations.where('landmark', are.equal_to('San Francisco'))
sf_map_data = sf.select('lat', 'long', 'name').relabel('name', 'labels')
Circle.map_table(sf_map_data, color='green')
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8.5.3. More Informative Maps: An Application of join

The bike stations are located in five different cities in the Bay Area. To distinguish the points by using a different color for each city, let’s start by using
group to identify all the cities and assign each one a color.
cities = stations.group('landmark').relabeled('landmark', 'city')
cities

city count
Mountain View 7
Palo Alto 5
Redwood City 7
San Francisco 35
San Jose 16
colors = cities.with_column('color', make_array('blue', 'red', 'green', 'orange',
'purple'))
colors

city count color

Mountain View 7 blue
Palo Alto 5 red
Redwood City 7 green
San Francisco 35 orange
San Jose 16 purple
Now we can join stations and colors by landmark, and then select the columns we need to draw a map.
joined = stations.join('landmark', colors, 'city')
colored = joined.select('lat', 'long', 'name', 'color').relabel('name', 'labels')
Marker.map_table(colored)
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Now the markers have five different colors for the five different cities.
To see where most of the bike rentals originate, let’s identify the start stations:
starts = commute.group('Start Station').sort('count', descending=True)
starts

Start Station count

San Francisco Caltrain (Townsend at 4th) 25858
San Francisco Caltrain 2 (330 Townsend) 21523
Harry Bridges Plaza (Ferry Building) 15543
Temporary Transbay Terminal (Howard at Beale) 14298
2nd at Townsend 13674
Townsend at 7th 13579
Steuart at Market 13215
Embarcadero at Sansome 12842
Market at 10th 11523
Market at Sansome 11023
... (60 rows omitted)
We can include the geographical data needed to map these stations, by first joining starts with stations:
station_starts = stations.join('name', starts, 'Start Station')
station_starts
name station_id lat long dockcount landmark installation count
2nd at 62 37.7853 ‑122.396 San 8/22/2013 7841
19 Francisco
Folsom
2nd at South 64 37.7823 ‑122.393 San 8/22/2013 9274
15 Francisco
Park
2nd at 61 37.7805 ‑122.39 San 8/22/2013 13674
27 Francisco
Townsend
5th at 57 37.7818 ‑122.405 San 8/21/2013 7394
15 Francisco
Howard
Adobe on 5 37.3314 ‑121.893 19 San Jose 8/5/2013 522
Almaden
Arena Green 14 37.3327 ‑121.9 19 San Jose 8/5/2013 590
/ SAP Center
Beale at 56 37.7923 ‑122.397 San 8/20/2013 8135
19 Francisco
Market
Broadway St 82 37.7985 ‑122.401 San 1/22/2014 7460
15 Francisco
at Battery St
California Ave
Caltrain 36 37.4291 ‑122.143 15 Palo Alto 8/14/2013 300
Station
Castro Street
and El 32 37.386 ‑122.084 11 Mountain
View 12/31/2013 1137
Camino Real
... (58 rows omitted)
Now we extract just the data needed for drawing our map, adding a color and an area to each station. The area is 0.3 times the count of the number
of rentals starting at each station, where the constant 0.3 was chosen so that the circles would appear at an appropriate scale on the map.
starts_map_data = station_starts.select('lat', 'long', 'name').with_columns(
'colors', 'blue',
'areas', station_starts.column('count') * 0.3
)
starts_map_data.show(3)
Circle.map_table(starts_map_data.relabel('name', 'labels'))

lat long name colors areas

37.7853 ‑122.396 2nd at Folsom blue 2352.3
37.7823 ‑122.393 2nd at South Park blue 2782.2
37.7805 ‑122.39 2nd at Townsend blue 4102.2
... (65 rows omitted)
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That huge blob in San Francisco shows that the eastern section of the city is the unrivaled capital of bike rentals in the Bay Area.

9. Randomness
In the previous chapters we developed skills needed to make insightful descriptions of data. Data scientists also have to be able to understand
randomness. For example, they have to be able to assign individuals to treatment and control groups at random, and then try to say whether any
observed differences in the outcomes of the two groups are simply due to the random assignment or genuinely due to the treatment.
In this chapter, we begin our analysis of randomness. To start off, we will use Python to make choices at random. In numpy there is a sub‑module
called random that contains many functions that involve random selection. One of these functions is called choice. It picks one item at random from
an array, and it is equally likely to pick any of the items. The function call is np.random.choice(array_name), where array_name is the name of the
array from which to make the choice.
Thus the following code evaluates to treatment with chance 50%, and control with chance 50%.
two_groups = make_array('treatment', 'control')
np.random.choice(two_groups)

'treatment'

The big difference between the code above and all the other code we have run thus far is that the code above doesn’t always return the same value.
It can return either treatment or control, and we don’t know ahead of time which one it will pick. We can repeat the process by providing a second
argument, the number of times to repeat the process.
np.random.choice(two_groups, 10)

array(['control', 'control', 'treatment', 'treatment', 'control',

'control', 'control', 'control', 'control', 'control'], dtype='<U9')

A fundamental question about random events is whether or not they occur. For example:
Did an individual get assigned to the treatment group, or not?
Is a gambler going to win money, or not?
Has a poll made an accurate prediction, or not?
Once the event has occurred, you can answer “yes” or “no” to all these questions. In programming, it is conventional to do this by labeling statements
as True or False. For example, if an individual did get assigned to the treatment group, then the statement, “The individual was assigned to the
treatment group” would be True. If not, it would be False.

Booleans and Comparison

In Python, Boolean values, named for the logician George Boole, represent truth and take only two possible values: True and False. Whether
problems involve randomness or not, Boolean values most often arise from comparison operators. Python includes a variety of operators that
compare values. For example, 3 is larger than 1 + 1.
3 > 1 + 1

True

The value True indicates that the comparison is valid; Python has confirmed this simple fact about the relationship between 3 and 1+1. The full set of
common comparison operators are listed below.
Comparison Operator True example False Example
Less than < 2<3 2<2
Greater than > 3>2 3>3
Less than or equal <= 2 <= 2 3 <= 2
Greater or equal >= 3 >= 3 2 >= 3
Equal == 3 == 3 3 == 2
Not equal != 3 != 2 2 != 2
Notice the two equal signs == in the comparison to determine equality. This is necessary because Python already uses = to mean assignment to a
name, as we have seen. It can’t use the same symbol for a different purpose. Thus if you want to check whether 5 is equal to the 10/2, then you have
to be careful: 5 = 10/2 returns an error message because Python assumes you are trying to assign the value of the expression 10/2 to a name that is
the numeral 5. Instead, you must use 5 == 10/2, which evaluates to True.
5 = 10/2

File "<ipython-input-5-e8c755f5e450>", line 1

5 = 10/2
^
SyntaxError: can't assign to literal

5 == 10/2

True

An expression can contain multiple comparisons, and they all must hold in order for the whole expression to be True. For example, we can express
that 1+1 is between 1 and 3 using the following expression.
1 < 1 + 1 < 3

True

The average of two numbers is always between the smaller number and the larger number. We express this relationship for the numbers x and y
below. You can try different values of x and y to confirm this relationship.
x = 12
y = 5
min(x, y) <= (x+y)/2 <= max(x, y)

True

Comparing Strings
Strings can also be compared, and their order is alphabetical. A shorter string is less than a longer string that begins with the shorter string.
'Dog' > 'Catastrophe' > 'Cat'

True

Let’s return to random selection. Recall the array two_groups which consists of just two elements, treatment and control. To see whether a
randomly assigned individual went to the treatment group, you can use a comparison:
np.random.choice(two_groups) == 'treatment'

True
As before, the random choice will not always be the same, so the result of the comparison won’t always be the same either. It will depend on whether
treatment or control was chosen. With any cell that involves random selection, it is a good idea to run the cell several times to get a sense of the
variability in the result.

Comparing an Array and a Value

Recall that we can perform arithmetic operations on many numbers in an array at once. For example, make_array(0, 5, 2)*2 is equivalent to
make_array(0, 10, 4). In similar fashion, if we compare an array and one value, each element of the array is compared to that value, and the
comparison evaluates to an array of Booleans.
tosses = make_array('Tails', 'Heads', 'Tails', 'Heads', 'Heads')
tosses == 'Heads'

array([False, True, False, True, True])

The numpy method count_nonzero evaluates to the number of non‑zero (that is, True) elements of the array.
np.count_nonzero(tosses == 'Heads')

9.1. Conditional Statements

In many situations, actions and results depends on a specific set of conditions being satisfied. For example, individuals in randomized controlled trials
receive the treatment if they have been assigned to the treatment group. A gambler makes money if she wins her bet.
In this section we will learn how to describe such situations using code. A conditional statement is a multi‑line statement that allows Python to
choose among different alternatives based on the truth value of an expression. While conditional statements can appear anywhere, they appear most
often within the body of a function in order to express alternative behavior depending on argument values.
A conditional statement always begins with an if header, which is a single line followed by an indented body. The body is only executed if the
expression directly following if (called the if expression) evaluates to a true value. If the if expression evaluates to a false value, then the body of the
if is skipped.

Let us start defining a function that returns the sign of a number.

def sign(x):

if x > 0:
return 'Positive'

sign(3)

'Positive'

This function returns the correct sign if the input is a positive number. But if the input is not a positive number, then the if expression evaluates to a
false value, and so the return statement is skipped and the function call has no value.
sign(-3)

So let us refine our function to return Negative if the input is a negative number. We can do this by adding an elif clause, where elif if Python’s
shorthand for the phrase “else, if”.
def sign(x):

if x > 0:
return 'Positive'

elif x < 0:
return 'Negative'
Now sign returns the correct answer when the input is ‑3:
sign(-3)

'Negative'

What if the input is 0? To deal with this case, we can add another elif clause:
def sign(x):

if x > 0:
return 'Positive'

elif x < 0:
return 'Negative'

elif x == 0:
return 'Neither positive nor negative'

sign(0)

'Neither positive nor negative'

Equivalently, we can replace the final elif clause by an else clause, whose body will be executed only if all the previous comparisons are false; that
is, if the input value is equal to 0.
def sign(x):

if x > 0:
return 'Positive'

elif x < 0:
return 'Negative'

else:
return 'Neither positive nor negative'

sign(0)

'Neither positive nor negative'

9.1.1. The General Form

A conditional statement can also have multiple clauses with multiple bodies, and only one of those bodies can ever be executed. The general format
of a multi‑clause conditional statement appears below.
if <if expression>:
<if body>
elif <elif expression 0>:
<elif body 0>
elif <elif expression 1>:
<elif body 1>
...
else:
<else body>

There is always exactly one if clause, but there can be any number of elif clauses. Python will evaluate the if and elif expressions in the headers
in order until one is found that is a true value, then execute the corresponding body. The else clause is optional. When an else header is provided, its
else body is executed only if none of the header expressions of the previous clauses are true. The else clause must always come at the end (or not at
all).

9.1.2. Example: Betting on a Die

Suppose I bet on a roll of a fair die. The rules of the game:
If the die shows 1 spot or 2 spots, I lose a dollar.
If the die shows 3 spots or 4 spots, I neither lose money nor gain money.
If the die shows 5 spots or 6 spots, I gain a dollar.
We will now use conditional statements to define a function one_bet that takes the number of spots on the roll and returns my net gain.
def one_bet(x):
"""Returns my net gain if the die shows x spots"""
if x <= 2:
return -1
elif x <= 4:
return 0
elif x <= 6:
return 1

Let’s check that the function does the right thing for each different number of spots.
one_bet(1), one_bet(2), one_bet(3), one_bet (4), one_bet(5), one_bet(6)

(-1, -1, 0, 0, 1, 1)

As a review of how conditional statements work, let’s see what one_bet does when the input is 3.
First it evaluates the if expression, which is 3 <= 2 which is False. So one_bet doesn’t execute the if body.
Then it evaluates the first elif expression, which is 3 <= 4, which is True. So one_bet executes the first elif body and returns 0.
Once the body has been executed, the process is complete. The next elif expression is not evaluated.
If for some reason we use an input greater than 6, then the if expression evaluates to False as do both of the elif expressions. So one_bet does not
execute the if body nor the two elif bodies, and there is no value when you make the call below.
one_bet(17)

To play the game based on one roll of a die, you can use np.random.choice to generate the number of spots and then use that as the argument to
one_bet. Run the cell a few times to see how the output changes.

one_bet(np.random.choice(np.arange(1, 7)))

-1

At this point it is natural to want to collect the results of all the bets so that we can analyze them. In the next section we develop a way to do this
without running the cell over and over again.

9.2. Iteration
It is often the case in programming – especially when dealing with randomness – that we want to repeat a process multiple times. For example, recall
the game of betting on one roll of a die with the following rules:
If the die shows 1 or 2 spots, my net gain is ‑1 dollar.
If the die shows 3 or 4 spots, my net gain is 0 dollars.
If the die shows 5 or 6 spots, my net gain is 1 dollar.
The function bet_on_one_roll takes no argument. Each time it is called, it simulates one roll of a fair die and returns the net gain in dollars.
def bet_on_one_roll():
"""Returns my net gain on one bet"""
x = np.random.choice(np.arange(1, 7)) # roll a die once and record the number of
spots
if x <= 2:
return -1
elif x <= 4:
return 0
elif x <= 6:
return 1
Playing this game once is easy:
bet_on_one_roll()

To get a sense of how variable the results are, we have to play the game over and over again. We could run the cell repeatedly, but that’s tedious, and
if we wanted to do it a thousand times or a million times, forget it.
A more automated solution is to use a for statement to loop over the contents of a sequence. This is called iteration. A for statement begins with the
word for, followed by a name we want to give each item in the sequence, followed by the word in, and ending with an expression that evaluates to a
sequence. The indented body of the for statement is executed once for each item in that sequence.
for animal in make_array('cat', 'dog', 'rabbit'):
print(animal)

cat
dog
rabbit

It is helpful to write code that exactly replicates a for statement, without using the for statement. This is called unrolling the loop.
A for statement simple replicates the code inside it, but before each iteration, it assigns a new value from the given sequence to the name we chose.
For example, here is an unrolled version of the loop above.
animal = make_array('cat', 'dog', 'rabbit').item(0)
print(animal)
animal = make_array('cat', 'dog', 'rabbit').item(1)
print(animal)
animal = make_array('cat', 'dog', 'rabbit').item(2)
print(animal)

cat
dog
rabbit

Notice that the name animal is arbitrary, just like any name we assign with =.
Here we use a for statement in a more realistic way: we print the results of betting five times on the die as described earlier. This is called simulating
the results of five bets. We use the word simulating to remind ourselves that we are not physically rolling dice and exchanging money but using
Python to mimic the process.
To repeat a process n times, it is common to use the sequence np.arange(n) in the for statement. It is also common to use a very short name for
each item. In our code we will use the name i to remind ourselves that it refers to an item.
for i in np.arange(5):
print(bet_on_one_roll())

1
-1
-1
1
1

In this case, we simply perform exactly the same (random) action several times, so the code in the body of our for statement does not actually refer
to i.

9.2.1. Augmenting Arrays

While the for statement above does simulate the results of five bets, the results are simply printed and are not in a form that we can use for
computation. Any array of results would be more useful. Thus a typical use of a for statement is to create an array of results, by augmenting the
array each time.
The append method in NumPy helps us do this. The call np.append(array_name, value) evaluates to a new array that is array_name augmented by
value. When you use append, keep in mind that all the entries of an array must have the same type.

pets = make_array('Cat', 'Dog')

np.append(pets, 'Another Pet')

array(['Cat', 'Dog', 'Another Pet'], dtype='<U11')

This keeps the array pets unchanged:

pets

array(['Cat', 'Dog'], dtype='<U3')

But often while using for loops it will be convenient to mutate an array – that is, change it – when augmenting it. This is done by assigning the
augmented array to the same name as the original.
pets = np.append(pets, 'Another Pet')
pets

array(['Cat', 'Dog', 'Another Pet'], dtype='<U11')

9.2.2. Example: Betting on 5 Rolls

We can now simulate five bets on the die and collect the results in an array that we will call the collection array. We will start out by creating an empty
array for this, and then append the outcome of each bet. Notice that the body of the for loop contains two statements. Both statements are executed
for each item in the given sequence.
outcomes = make_array()

for i in np.arange(5):
outcome_of_bet = bet_on_one_roll()
outcomes = np.append(outcomes, outcome_of_bet)

outcomes

array([-1., -1., 1., 1., -1.])

Let us rewrite the cell with the for statement unrolled:

outcomes = make_array()

i = np.arange(5).item(0)
outcome_of_bet = bet_on_one_roll()
outcomes = np.append(outcomes, outcome_of_bet)

i = np.arange(5).item(1)
outcome_of_bet = bet_on_one_roll()
outcomes = np.append(outcomes, outcome_of_bet)

i = np.arange(5).item(2)
outcome_of_bet = bet_on_one_roll()
outcomes = np.append(outcomes, outcome_of_bet)

i = np.arange(5).item(3)
outcome_of_bet = bet_on_one_roll()
outcomes = np.append(outcomes, outcome_of_bet)

i = np.arange(5).item(4)
outcome_of_bet = bet_on_one_roll()
outcomes = np.append(outcomes, outcome_of_bet)

outcomes

array([ 1., 0., 0., -1., 1.])

The contents of the array are likely to be different from the array that we got by running the previous cell, but that is because of randomness in rolling
the die. The process for creating the array is exactly the same.
By capturing the results in an array we have given ourselves the ability to use array methods to do computations. For example, we can use
np.count_nonzero to count the number of times money changed hands.

np.count_nonzero(outcomes)

9.2.3. Example: Betting on 300 Rolls

Iteration is a powerful technique. For example, we can see the variation in the results of 300 bets by running exactly the same code for 300 bets
instead of five.
outcomes = make_array()

for i in np.arange(300):
outcome_of_bet = bet_on_one_roll()
outcomes = np.append(outcomes, outcome_of_bet)

The array outcomes contains the results of all 300 bets.

len(outcomes)

300

To see how often the three different possible results appeared, we can use the array outcomes and Table methods.
outcome_table = Table().with_column('Outcome', outcomes)
outcome_table.group('Outcome').barh(0)

Not surprisingly, each of the three outcomes ‑1, 0, and 1 appeared about about 100 of the 300 times, give or take. We will examine the “give or take”
amounts more closely in later chapters.

9.3. Simulation
Simulation is the process of using a computer to mimic a physical experiment. In this class, those experiments will almost invariably involve chance.
We have seen how to simulate the results of tosses of a coin. The steps in that simulation were examples of the steps that will constitute every
simulation we do in this course. In this section we will set out those steps and follow them in examples.

9.3.1. The Process

Step 1: What to Simulate
Decide which quantity you want to simulate. For example, you might decide that you want to simulate the outcomes of tosses of a coin. Each
simulated value will be a Head or a Tail.
Step 2: Simulating One Value
Figure out how to simulate one value of the quantity you specified in Step 1. In our example, you have to figure out how to simulate the outcome of
one toss of a coin. If your quantity is more complicated, you might need several lines of code to come up with one simulated value. Typically, we will
define a function that returns the simulated value.
Step 3: Number of Repetitions
Decide how many times you want to simulate the quantity. You will have to repeat the simulation in Step 2 that many times. In one of our earlier
examples we had decided to simulate the outcomes of 1000 tosses of a coin, and so we needed 1000 repetitions of generating the outcome of a
single toss.
Step 4: Simulating Multiple Values
Finally, put it all together as follows.
Create an empty array in which to collect all the simulated values. We will call this the collection array.
Create a “repetitions sequence,” that is, a sequence whose length is the number of repetitions you specified in Step 3. For n repetitions we will
almost always use the sequence np.arange(n).
Create a for loop. For each element of the repetitions sequence:
Simulate one value by using the function you wrote in Step 2.
Augment the collection array with this simulated value.
That’s it! Once you have carried out the steps above, your simulation is done. The collection array contains all the simulated values.
At this point you can use the collection array as you would any other array. You can count how many simulated values fall into a particular category,
place the array in the column of a table and visualize the distribution of the simulated values, and so on.

9.3.2. Example: Number of Heads in 100 Tosses

It is natural to expect that in 100 tosses of a coin, there will be 50 heads, give or take a few.
But how many is “a few”? What’s the chance of getting exactly 50 heads? Questions like these matter in data science not only because they are
about interesting aspects of randomness, but also because they can be used in analyzing experiments where assignments to treatment and control
groups are decided by the toss of a coin.
In this example we will simulate the number of heads in 100 tosses of a coin. The histogram of our results will give us some insight into how many
heads are likely.
Let’s get started on the simulation, following the steps above.
Step 1: What to Simulate
The quantity we are going to simulate is the number of heads in 100 tosses.
Step 2: Simulating One Value
We have to figure out how to make one set of 100 tosses and count the number of heads. Let’s start by creating a coin.
coin = make_array('Heads', 'Tails')

In our earlier example we used np.random.choice and a for loop to generate multiple tosses. But sets of coin tosses are needed so often in data
science that np.random.choice simulates them for us if we include a second argument that is the number of times to toss.
Here are the results of 10 tosses.
ten_tosses = np.random.choice(coin, 10)
ten_tosses
array(['Heads', 'Tails', 'Heads', 'Tails', 'Tails', 'Heads', 'Tails',
'Tails', 'Tails', 'Heads'], dtype='<U5')

We can count the number of heads by using np.count_nonzero as before:

np.count_nonzero(ten_tosses == 'Heads')

Our goal is to simulate the number of heads in 100 tosses, not 10. To do that we can just repeat the same code, replacing 10 by 100.
outcomes = np.random.choice(coin, 100)
num_heads = np.count_nonzero(outcomes == 'Heads')
num_heads

Since we will want to do this multiple times, let’s define a function that returns the simulated value of the number of heads. We can do this using the
code developed in the cell above.
def one_simulated_value():
outcomes = np.random.choice(coin, 100)
return np.count_nonzero(outcomes == 'Heads')

Step 3: Number of Repetitions

How many repetitions we will use is up to us. The more we use, the more reliable our simulations will be, but the longer it will take to run the code.
Python is pretty fast at tossing coins, so let’s go for 20,000 repetitions. That means we are going to do the following 20,000 times:
Toss a coin 100 times and count the number of heads.
That’s a lot of tossing! It’s good that we have Python to do it for us.
Step 4: Simulating Multiple Values
We are ready to create an array of 20,000 simulated values of the number of heads in 100 tosses of a coin.
num_repetitions = 20000 # number of repetitions

heads = make_array() # empty collection array

for i in np.arange(num_repetitions): # repeat the process num_repetitions times

new_value = one_simulated_value() # simulate one value using the function defined
heads = np.append(heads, new_value) # augment the collection array with the
simulated value

# That's it! The simulation is done.

Check that the array heads contains 20,000 entries, one for each repetition of the experiment.
len(heads)

20000

To get a sense of the variability in the number of heads in 100 tosses, we can collect the results in a table and draw a histogram.
simulation_results = Table().with_columns(
'Repetition', np.arange(1, num_repetitions + 1),
'Number of Heads', heads
)

simulation_results.show(3)
Repetition Number of Heads
1 44
2 54
3 44
... (19997 rows omitted)
simulation_results.hist('Number of Heads', bins = np.arange(30.5, 69.6, 1))

Each bin has width 1 and is centered at each value of the number of heads.
Not surprisingly, the histogram looks roughly symmetric around 50 heads. The height of the bar at 50 is about 8% per unit. Since each bin is 1 unit
wide, this is the same as saying that about 8% of the repetitions produced exactly 50 heads. That’s not a huge percent, but it’s the largest compared
to the percent at every other number of heads.
The histogram also shows that in almost all of the repetitions, the number of heads in 100 tosses was somewhere between 35 and 65. Indeed, the
bulk of the repetitions produced numbers of heads in the range 45 to 55.
While in theory it is possible that the number of heads can be anywhere between 0 and 100, the simulation shows that the range of probable values is
much smaller.
This is an instance of a more general phenomenon about the variability in coin tossing, as we will see later in the course.

9.3.3. Example: Moves in Monopoly

Each move in the game Monopoly is determined by the total number of spots of two rolls of a die. If you play Monopoly, what should you expect to
get when you roll the die two times?
We can explore this by simulating the sum of two rolls of a die. We will run the simulation 10,000 times. Notice that in this paragraph we have
completed Steps 1 and 3 of our simulation process.
Step 2 is the one in which we write a function to simulate the total number of spots in one pair of rolls. First, let’s plan our code. We will create an
array containing the numbers 1 through 6, draw two times from the array at random with replacement, and add the two numbers drawn.
die = np.arange(1, 7)
sum(np.random.choice(die, 2))

We can use the array die and the expression above to define a function that simulates one move in Monopoly.
def one_simulated_move():
return sum(np.random.choice(die, 2))

Now we can create an array of 10000 simulated Monopoly moves, by starting with an empty collection array and augmenting it by each new
simulated move.
num_repetitions = 10000

moves = make_array()
for i in np.arange(num_repetitions):
new_move = one_simulated_move()
moves = np.append(moves, new_move)

Here is a histogram of the results.

results = Table().with_columns(
'Repetition', np.arange(1, num_repetitions + 1),
'Sum of Two Rolls', moves
)

results.hist('Sum of Two Rolls', bins = np.arange(1.5, 12.6, 1))

Seven is the most common value, with the frequencies falling off symmetrically on either side.

9.4. The Monty Hall Problem

This problem has flummoxed many people over the years, mathematicians included. Let’s see if we can work it out by simulation.
The setting is derived from a television game show called “Let’s Make a Deal”. Monty Hall hosted this show in the 1960’s, and it has since led to a
number of spin‑offs. An exciting part of the show was that while the contestants had the chance to win great prizes, they might instead end up with
“zonks” that were less desirable. This is the basis for what is now known as the Monty Hall problem.
The setting is a game show in which the contestant is faced with three closed doors. Behind one of the doors is a fancy car, and behind each of the
other two there is a goat. The contestant doesn’t know where the car is, and has to attempt to find it under the following rules.
The contestant makes an initial choice, but that door isn’t opened.
At least one of the other two doors must have a goat behind it. Monty opens one of these doors to reveal a goat, displayed in all its glory in
Wikipedia:

There are two doors left, one of which was the contestant’s original choice. One of the doors has the car behind it, and the other one has a goat.
The contestant now gets to choose which of the two doors to open.
The contestant has a decision to make. Which door should she choose to open, if she wants the car? Should she stick with her initial choice, or
switch to the other door? That is the Monty Hall problem.

9.4.1. The Solution

In any problem involving chances, the assumptions about randomness are important. It’s reasonable to assume that there is a 1/3 chance that the
contestant’s initial choice is the door that has the car behind it.
The solution to the problem is quite straightforward under this assumption, though the straightforward solution doesn’t convince everyone. Here it is
anyway.
The chance that the car is behind the originally chosen door is 1/3.
The car is behind either the originally chosen door or the door that remains. It can’t be anywhere else.
Therefore, the chance that the car is behind the door that remains is 2/3.
Therefore, the contestant should switch.
That’s it. End of story.
Not convinced? Then let’s simulate the game and see how the results turn out.

9.4.2. Simulation
The simulation will be more complex that those we have done so far. Let’s break it down.
Step 1: What to Simulate
For each play we will simulate what’s behind all three doors:
the one the contestant first picks
the one that Monty opens
the remaining door
So we will be keeping track of three quantitites, not just one.
Step 2: Simulating One Play
As is often the case in simulating a game, the bulk of the work consists of simulating one play of the game. This involves several pieces.
The goats: We start by setting up an array goats that contains unimaginative names for the two goats.
goats = make_array('first goat', 'second goat')

To help Monty conduct the game, we are going to have to identify which goat is selected and which one is revealed behind the open door. The
function other_goat takes one goat and returns the other.
def other_goat(x):
if x == 'first goat':
return 'second goat'
elif x == 'second goat':
return 'first goat'

other_goat('first goat'), other_goat('second goat'), other_goat('watermelon')

('second goat', 'first goat', None)

The string watermelon is not the name of one of the goats, so when watermelon is the input then other_goat does nothing.
The options: The array hidden_behind_doors contains the three things that are behind the doors.
hidden_behind_doors = np.append(goats, 'car')
hidden_behind_doors

array(['first goat', 'second goat', 'car'], dtype='<U11')

We are now ready to simulate one play. To do this, we will define a function monty_hall_game that takes no arguments. When the function is called, it
plays Monty’s game once and returns a list consisting of:
the contestant’s guess
what Monty reveals when he opens a door
what remains behind the other door
The game starts with the contestant choosing one door at random. In doing so, the contestant makes a random choice from among the first goat, the
second goat, and the car.
If the contestant happens to pick one of the goats, then the other goat is revealed and the car is behind the remaining door.
If the contestant happens to pick the car, then Monty reveals one of the goats and the other goat is behind the remaining door.
def monty_hall_game():
"""Return
[contestant's guess, what Monty reveals, what remains behind the other door]"""

contestant_guess = np.random.choice(hidden_behind_doors)

if contestant_guess == 'first goat':

return [contestant_guess, 'second goat', 'car']

if contestant_guess == 'second goat':

return [contestant_guess, 'first goat', 'car']

if contestant_guess == 'car':
revealed = np.random.choice(goats)
return [contestant_guess, revealed, other_goat(revealed)]

Let’s play! Run the cell several times and see how the results change.
monty_hall_game()

['car', 'first goat', 'second goat']

Step 3: Number of Repetitions

To gauge the frequency with which the different results occur, we have to play the game many times and collect the results. Let’s run 10,000
repetitions.
Step 4: Simulating Multiple Repetitions
It’s time to run the whole simulation. But unlike our previous simulations in which each simulation produced a single value, in this example we simulate
a list of three values each time.
We will treat this simulated list as a row of a table. So instead of starting with an empty array and augmenting it with each new simulated value, we
will start with an empty table and augment the table with each new simulated row. Each row will contain the complete result of one play.
One way to grow a table by adding a new row is to use the append method. If my_table is a table and new_row is a list containing the entries in a new
row, then my_table.append(new_row) adds the new row to the bottom of my_table.
Note that append does not create a new table. It changes my_table to have one more row than it did before.
We will start with a collection table games that has three empty columns. We can do this by just specifying a list of the column labels in the same
order in which monty_hall_game returns the result of one game.
Now we can add 10,000 rows to games. Each row will represent the result of one play of Monty’s game.
# empty collection table
games = Table(['Guess', 'Revealed', 'Remaining'])

# Play the game 10000 times and

# record the results in the table games

for i in np.arange(10000):
games.append(monty_hall_game())

The simulation is done. Notice how short the code is. The majority of the work was done in simulating the outcome of one game.
games.show(3)
Guess Revealed Remaining
first goat second goat car
first goat second goat car
car first goat second goat
... (9997 rows omitted)

9.4.3. Visualization
To see whether the contestant should stick with her original choice or switch, let’s see how frequently the car is behind each of her two options.
It is no surprise that the three doors appear about equally often as the contestant’s original guess.
original_choice = games.group('Guess')
original_choice

Guess count
car 3319
first goat 3311
second goat 3370
Once Monty has eliminated a goat, how often is the car behind the remaining door?
remaining_door = games.group('Remaining')
remaining_door

Remaining count
car 6681
first goat 1676
second goat 1643
As our earlier solution said, the car is behind the remaining door two‑thirds of the time, to a pretty good approximation. The contestant is twice as
likely to get the car if she switches than if she sticks with her original choice.
To see this graphically, we can join the two tables above and draw overlaid bar charts.
joined = original_choice.join('Guess', remaining_door, 'Remaining')
combined = joined.relabeled(0, 'Item').relabeled(1, 'Original Door').relabeled(2,
'Remaining Door')
combined

Item Original Door Remaining Door

car 3319 6681
first goat 3311 1676
second goat 3370 1643
combined.barh(0)
Notice how the three blue bars are almost equal – the original choice is equally likely to be any of the three available items. But the gold bar
corresponding to Car is twice as long as the blue.
The simulation confirms that the contestant is twice as likely to win if she switches.

9.5. Finding Probabilities

Over the centuries, there has been considerable philosophical debate about what probabilities are. Some people think that probabilities are relative
frequencies; others think they are long run relative frequencies; still others think that probabilities are a subjective measure of their own personal
degree of uncertainty.
In this course, most probabilities will be relative frequencies, though many will have subjective interpretations. Regardless, the ways in which
probabilities are calculated and combined are consistent across the different interpretations.
By convention, probabilities are numbers between 0 and 1, or, equivalently, 0% and 100%. Impossible events have probability 0. Events that are
certain have probability 1.
Math is the main tool for finding probabilities exactly, though computers are useful for this purpose too. Simulation can provide excellent
approximations, with high probability. In this section, we will informally develop a few simple rules that govern the calculation of probabilities. In
subsequent sections we will return to simulations to approximate probabilities of complex events.
We will use the standard notation $P(\mbox{event})$ to denote the probability that “event” happens, and we will use the words “chance” and
“probability” interchangeably.

9.5.1. When an Event Doesn’t Happen

If the chance that event happens is 40%, then the chance that it doesn’t happen is 60%. This natural calculation can be described in general as
follows:
\[ P(\mbox{an event doesn't happen}) ~=~ 1 ‑ P(\mbox{the event happens}) \]

9.5.2. When All Outcomes are Equally Likely

If you are rolling an ordinary die, a natural assumption is that all six faces are equally likely. Under this assumption, the probabilities of how one roll
comes out can be easily calculated as a ratio. For example, the chance that the die shows an even number is
\[ \frac{\mbox{number of even faces}}{\mbox{number of all faces}} ~=~ \frac{\#\{2, 4, 6\}}{\#\{1, 2, 3, 4, 5, 6\}} ~=~ \frac{3}{6} \]
Similarly,
\[ P(\mbox{die shows a multiple of 3}) ~=~ \frac{\#\{3, 6\}}{\#\{1, 2, 3, 4, 5, 6\}} ~=~ \frac{2}{6} \]
In general, if all outcomes are equally likely,
\[ P(\mbox{an event happens}) ~=~ \frac{\#\{\mbox{outcomes that make the event happen}\}} {\#\{\mbox{all outcomes}\}} \]
Not all random phenomena are as simple as one roll of a die. The two main rules of probability, developed below, allow mathematicians to find
probabilities even in complex situations.

9.5.3. When Two Events Must Both Happen

Suppose you have a box that contains three tickets: one red, one blue, and one green. Suppose you draw two tickets at random without replacement;
that is, you shuffle the three tickets, draw one, shuffle the remaining two, and draw another from those two. What is the chance you get the green
ticket first, followed by the red one?
There are six possible pairs of colors: RB, BR, RG, GR, BG, GB (we’ve abbreviated the names of each color to just its first letter). All of these are
equally likely by the sampling scheme, and only one of them (GR) makes the event happen. So
\[ P(\mbox{green first, then red}) ~=~ \frac{\#\{\mbox{GR}\}}{\#\{\mbox{RB, BR, RG, GR, BG, GB}\}} ~=~ \frac{1}{6} \]
But there is another way of arriving at the answer, by thinking about the event in two stages. First, the green ticket has to be drawn. That has chance \
(1/3\), which means that the green ticket is drawn first in about $1/3$ of all repetitions of the experiment. But that doesn’t complete the event. Among
the 1/3 of repetitions when green is drawn first, the red ticket has to be drawn next. That happens in about $1/2$ of those repetitions, and so:
\[ P(\mbox{green first, then red}) ~=~ \frac{1}{2} ~\mbox{of}~ \frac{1}{3} ~=~ \frac{1}{6} \]
This calculation is usually written “in chronological order,” as follows.
\[ P(\mbox{green first, then red}) ~=~ \frac{1}{3} ~\times~ \frac{1}{2} ~=~ \frac{1}{6} \]
The factor of $1/2$ is called ” the conditional chance that the red ticket appears second, given that the green ticket appeared first.”
In general, we have the multiplication rule:
\[ P(\mbox{two events both happen}) ~=~ P(\mbox{one event happens}) \times P(\mbox{the other event happens, given that the first one happened})
\]
Thus, when there are two conditions – one event must happen, as well as another – the chance is a fraction of a fraction, which is smaller than either
of the two component fractions. The more conditions that have to be satisfied, the less likely they are to all be satisfied.

9.5.4. When an Event Can Happen in Two Different Ways

Suppose instead we want the chance that one of the two tickets is green and the other red. This event doesn’t specify the order in which the colors
must appear. So they can appear in either order.
A good way to tackle problems like this is to partition the event so that it can happen in exactly one of several different ways. The natural partition of
“one green and one red” is: GR, RG.
Each of GR and RG has chance $1/6$ by the calculation above. So you can calculate the chance of “one green and one red” by adding them up.
\[ P(\mbox{one green and one red}) ~=~ P(\mbox{GR}) + P(\mbox{RG}) ~=~ \frac{1}{6} + \frac{1}{6} ~=~ \frac{2}{6} \]
In general, we have the addition rule:
\[ P(\mbox{an event happens}) ~=~ P(\mbox{first way it can happen}) + P(\mbox{second way it can happen}) ~~~ \mbox{} \]
provided the event happens in exactly one of the two ways.
Thus, when an event can happen in one of two different ways, the chance that it happens is a sum of chances, and hence bigger than the chance of
either of the individual ways.
The multiplication rule has a natural extension to more than two events, as we will see below. So also the addition rule has a natural extension to
events that can happen in one of several different ways.
We end the section with examples that use combinations of all these rules.

9.5.5. At Least One Success

Data scientists often work with random samples from populations. A question that sometimes arises is about the likelihood that a particular individual
in the population is selected to be in the sample. To work out the chance, that individual is called a “success,” and the problem is to find the chance
that the sample contains a success.
To see how such chances might be calculated, we start with a simpler setting: tossing a coin two times.
If you toss a coin twice, there are four equally likely outcomes: HH, HT, TH, and TT. We have abbreviated “Heads” to H and “Tails” to T. The chance of
getting at least one head in two tosses is therefore 3/4.
Another way of coming up with this answer is to work out what happens if you don’t get at least one head. That is when both the tosses land tails. So
\[ P(\mbox{at least one head in two tosses}) ~=~ 1 ‑ P(\mbox{both tails}) ~=~ 1 ‑ \frac{1}{4} ~=~ \frac{3}{4} \]
Notice also that
\[ P(\mbox{both tails}) ~=~ \frac{1}{4} ~=~ \frac{1}{2} \cdot \frac{1}{2} ~=~ \left(\frac{1}{2}\right)^2 \]
by the multiplication rule.
These two observations allow us to find the chance of at least one head in any given number of tosses. For example,
\[ P(\mbox{at least one head in 17 tosses}) ~=~ 1 ‑ P(\mbox{all 17 are tails}) ~=~ 1 ‑ \left(\frac{1}{2}\right)^{17} \]
And now we are in a position to find the chance that the face with six spots comes up at least once in rolls of a die.
For example,
\[ P(\mbox{a single roll is not 6}) ~=~ 1 ‑ P(6) ~=~ \frac{5}{6} \]
Therefore,
\[ P(\mbox{at least one 6 in two rolls}) ~=~ 1 ‑ P(\mbox{both rolls are not 6}) ~=~ 1 ‑ \left(\frac{5}{6}\right)^2 \]
and
\[ P(\mbox{at least one 6 in 17 rolls}) ~=~ 1 ‑ \left(\frac{5}{6}\right)^{17} \]
The table below shows these probabilities as the number of rolls increases from 1 to 50.
rolls = np.arange(1, 51, 1)
results = Table().with_columns(
'Rolls', rolls,
'Chance of at least one 6', 1 - (5/6)**rolls
)
results

Rolls Chance of at least one 6

1 0.166667
2 0.305556
3 0.421296
4 0.517747
5 0.598122
6 0.665102
7 0.720918
8 0.767432
9 0.806193
10 0.838494
... (40 rows omitted)
The chance that a 6 appears at least once rises rapidly as the number of rolls increases.
results.scatter('Rolls')

In 50 rolls, you are almost certain to get at least one 6.

results.where('Rolls', are.equal_to(50))

Rolls Chance of at least one 6

50 0.99989
Calculations like these can be used to find the chance that a particular individual is selected in a random sample. The exact calculation will depend on
the sampling scheme. But what we have observed above can usually be generalized: increasing the size of the random sample increases the chance
that an individual is selected.

10. Sampling and Empirical Distributions

An important part of data science consists of making conclusions based on the data in random samples. In order to correctly interpret their results,
data scientists have to first understand exactly what random samples are.
In this chapter we will take a more careful look at sampling, with special attention to the properties of large random samples.
Let’s start by drawing some samples. Our examples are based on the top_movies_2017.csv data set.
top1 = Table.read_table(path_data + 'top_movies_2017.csv')
top2 = top1.with_column('Row Index', np.arange(top1.num_rows))
top = top2.move_to_start('Row Index')

top.set_format(make_array(3, 4), NumberFormatter)

Row Title Studio Gross Gross Year

Index (Adjusted)
0 Gone with the Wind MGM 198,676,459 1,796,176,700 1939
1 Star Wars Fox 460,998,007 1,583,483,200 1977
2 The Sound of Music Fox 158,671,368 1,266,072,700 1965
3 E.T.: The Extra‑Terrestrial Universal 435,110,554 1,261,085,000 1982
4 Titanic Paramount 658,672,302 1,204,368,000 1997
5 The Ten Commandments Paramount 65,500,000 1,164,590,000 1956
6 Jaws Universal 260,000,000 1,138,620,700 1975
7 Doctor Zhivago MGM 111,721,910 1,103,564,200 1965
8 The Exorcist Warner 232,906,145 983,226,600 1973
Brothers
9 Snow White and theDwarves Seven Disney 184,925,486 969,010,000 1937
... (190 rows omitted)

Sampling Rows of a Table

Each row of a data table represents an individual; in top, each individual is a movie. Sampling individuals can thus be achieved by sampling the rows
of a table.
The contents of a row are the values of different variables measured on the same individual. So the contents of the sampled rows form samples of
values of each of the variables.

Deterministic Samples
When you simply specify which elements of a set you want to choose, without any chances involved, you create a deterministic sample.
You have done this many times, for example by using take:
top.take(make_array(3, 18, 100))
Row Index Title Studio Gross Gross (Adjusted) Year
3 E.T.: The Extra‑Terrestrial Universal 435,110,554 1,261,085,000 1982
18 The Lion King Buena Vista 422,783,777 792,511,700 1994
100 The Hunger Games Lionsgate 408,010,692 452,174,400 2012
You have also used where:
top.where('Title', are.containing('Harry Potter'))

Row Title Studio Gross Year

Gross (Adjusted)
Index
74 Harry Potter and the Sorcerer's Warner 317,575,550 497,066,400 2001
Stone Brothers
114 Harry Potter and the Deathly Warner 381,011,219 426,630,300 2011
Hallows Part 2 Brothers
131 Harry Potter and the GobletFireof BrothersWarner 290,013,036 401,608,200 2005
133 Harry Potter and the Chamber of Warner
Secrets Brothers 261,988,482 399,302,200 2002
154 Harry Potter and the OrderPhoenix
of the Warner
Brothers 292,004,738 377,314,200 2007
175 Harry Potter and the Half‑Blood Warner
Prince Brothers 301,959,197 359,788,300 2009
177 Harry Potter and the Prisoner of Warner
Azkaban Brothers 249,541,069 357,233,500 2004
While these are samples, they are not random samples. They don’t involve chance.

Probability Samples
For describing random samples, some terminology will be helpful.
A population is the set of all elements from whom a sample will be drawn.
A probability sample is one for which it is possible to calculate, before the sample is drawn, the chance with which any subset of elements will enter
the sample.
In a probability sample, all elements need not have the same chance of being chosen.

A Random Sampling Scheme

For example, suppose you choose two people from a population that consists of three people A, B, and C, according to the following scheme:
Person A is chosen with probability 1.
One of Persons B or C is chosen according to the toss of a coin: if the coin lands heads, you choose B, and if it lands tails you choose C.
This is a probability sample of size 2. Here are the chances of entry for all non‑empty subsets:
A: 1
B: 1/2
C: 1/2
AB: 1/2
AC: 1/2
BC: 0
ABC: 0

Person A has a higher chance of being selected than Persons B or C; indeed, Person A is certain to be selected. Since these differences are known
and quantified, they can be taken into account when working with the sample.
A Systematic Sample
Imagine all the elements of the population listed in a sequence. One method of sampling starts by choosing a random position early in the list, and
then evenly spaced positions after that. The sample consists of the elements in those positions. Such a sample is called a systematic sample.
Here we will choose a systematic sample of the rows of top. We will start by picking one of the first 10 rows at random, and then we will pick every
10th row after that.
"""Choose a random start among rows 0 through 9;
then take every 10th row."""

start = np.random.choice(np.arange(10))
top.take(np.arange(start, top.num_rows, 10))

Row Title Studio Gross (Adjusted)Gross Year

Index
6 Jaws Universal 260,000,000 1,138,620,700 1975
16 Jurassic Park Universal 402,453,882 817,186,200 1993
26 Mary Poppins Disney 102,272,727 695,036,400 1964
36 Love Story Paramount 106,397,186 622,283,500 1970
46 The Robe Fox 36,000,000 581,890,900 1953
56 Rogue One: A Star
Wars Story Buena Vista 532,177,324 537,326,000 2016
66 The Dark Knight Rises Warner Brothers 448,139,099 511,902,300 2012
76 Close theEncounters of
Third Kind Columbia 132,088,635 494,066,600 1977
86 RevengeTransformers:
of the Fallen Paramount/Dreamworks 402,111,870 479,179,200 2009
96 Toy Story 3 Buena Vista 415,004,880 464,074,600 2010
... (10 rows omitted)
Run the cell a few times to see how the output varies.
This systematic sample is a probability sample. In this scheme, all rows have chance $1/10$ of being chosen. For example, Row 23 is chosen if and
only if Row 3 is chosen, and the chance of that is $1/10$.
But not all subsets have the same chance of being chosen. Because the selected rows are evenly spaced, most subsets of rows have no chance of
being chosen. The only subsets that are possible are those that consist of rows all separated by multiples of 10. Any of those subsets is selected with
chance 1/10. Other subsets, such as a subset containing both the 15th and 16th rows of the table, or any subset of size more than 10, are selected
with chance 0.

Random Samples Drawn With or Without Replacement

In this course, we will mostly deal with the two most straightforward methods of sampling.
The first is random sampling with replacement, which (as we have seen earlier) is the default behavior of np.random.choice when it samples from an
array.
The other, called a “simple random sample”, is a sample drawn at random without replacement. Sampled individuals are not replaced in the
population before the next individual is drawn. This is the kind of sampling that happens when you deal a hand from a deck of cards, for example. To
use np.random.choice for simple random sampling, you must include the argument replace=False.
In this chapter, we will use simulation to study the behavior of large samples drawn at random with or without replacement.

Convenience Samples
Drawing a random sample requires care and precision. It is not haphazard even though that is a colloquial meaning of the word "random". If you stand
at a street corner and take as your sample the first ten people who pass by, you might think you're sampling at random because you didn't choose
who walked by. But it's not a random sample – it's a *sample of convenience*. You didn't know ahead of time the probability of each person entering
the sample; perhaps you hadn't even specified exactly who was in the population.

10.1. Empirical Distributions

In data science, the word “empirical” means “observed”. Empirical distributions are distributions of observed data, such as data in random samples.
In this section we will generate data and see what the empirical distribution looks like.
Our setting is a simple experiment: rolling a die multiple times and keeping track of which face appears. The table die contains the numbers of spots
on the faces of a die. All the numbers appear exactly once, as we are assuming that the die is fair.
die = Table().with_column('Face', np.arange(1, 7, 1))
die

Face
1
2
3
4
5
6

10.1.1. A Probability Distribution

The histogram below helps us visualize the fact that every face appears with probability 1/6. We say that the histogram shows the distribution of
probabilities over all the possible faces. Since all the bars represent the same percent chance, the distribution is called uniform on the integers 1
through 6.
die_bins = np.arange(0.5, 6.6, 1)
die.hist(bins = die_bins)

Variables whose successive values are separated by the same fixed amount, such as the values on rolls of a die (successive values separated by 1),
fall into a class of variables that are called discrete. The histogram above is called a discrete histogram. Its bins are specified by the array die_bins
and ensure that each bar is centered over the corresponding integer value.
It is important to remember that the die can’t show 1.3 spots, or 5.2 spots – it always shows an integer number of spots. But our visualization spreads
the probability of each value over the area of a bar. While this might seem a bit arbitrary at this stage of the course, it will become important later
when we overlay smooth curves over discrete histograms.
Before going further, let’s make sure that the numbers on the axes make sense. The probability of each face is 1/6, which is 16.67% when rounded to
two decimal places. The width of each bin is 1 unit. So the height of each bar is 16.67% per unit. This agrees with the horizontal and vertical scales of
the graph.

10.1.2. Empirical Distributions

The distribution above consists of the theoretical probability of each face. It is called a probability distribution and is not based on observed data. It
can be studied and understood without any dice being rolled.
Empirical distributions, on the other hand, are distributions of observed data. They can be visualized by empirical histograms.
Let us get some data by simulating rolls of a die. This can be done by sampling at random with replacement from the integers 1 through 6. We have
used np.random.choice for such simulations before. But now we will introduce a Table method for doing this. This will make it easier for us to use our
familiar Table methods for visualization.
The Table method is called sample. It draws at random with replacement from the rows of a table. Its argument is the sample size, and it returns a
table consisting of the rows that were selected. An optional argument with_replacement=False specifies that the sample should be drawn without
replacement. But that does not apply to rolling a die.
Here are the results of 10 rolls of a die.
die.sample(10)

Face
2
4
5
5
1
6
1
4
6
5
We can use the same method to simulate as many rolls as we like, and then draw empirical histograms of the results. Because we are going to do this
repeatedly, we define a function empirical_hist_die that takes the sample size as its argument, rolls a die as many times as the argument, and then
draws a histogram of the observed results.
def empirical_hist_die(n):
die.sample(n).hist(bins = die_bins)

10.1.3. Empirical Histograms

Here is an empirical histogram of 10 rolls. It doesn’t look very much like the probability histogram above. Run the cell a few times to see how it varies.
empirical_hist_die(10)
When the sample size increases, the empirical histogram begins to look more like the histogram of theoretical probabilities.
empirical_hist_die(100)

empirical_hist_die(1000)

As we increase the number of rolls in the simulation, the area of each bar gets closer to 16.67%, which is the area of each bar in the probability
histogram.

10.1.4. The Law of Averages

What we have observed above is an instance of a general rule called the law of averages:
If a chance experiment is repeated independently and under identical conditions, then, in the long run, the proportion of times that an event occurs
gets closer and closer to the theoretical probability of the event.
For example, in the long run, the proportion of times the face with four spots appears gets closer and closer to 1/6.
Here “independently and under identical conditions” means that every repetition is performed in the same way regardless of the results of all the
other repetitions.
Under these conditions, the law above implies that if the chance experiment is repeated a large number of times then the proportion of times that an
event occurs is very likely to be close to the theoretical probability of the event.
10.2. Sampling from a Population
The law of averages also holds when the random sample is drawn from individuals in a large population.
As an example, we will study a population of flight delay times. The table united contains data for United Airlines domestic flights departing from San
Francisco in the summer of 2015. The data are made publicly available by the Bureau of Transportation Statistics in the United States Department of
Transportation.
There are 13,825 rows, each corresponding to a flight. The columns are the date of the flight, the flight number, the destination airport code, and the
departure delay time in minutes. Some delay times are negative: those flights left early.
united = Table.read_table(path_data + 'united_summer2015.csv')
united

Date Flight Number Destination Delay

6/1/15 73 HNL 257
6/1/15 217 EWR 28
6/1/15 237 STL ‑3
6/1/15 250 SAN 0
6/1/15 267 PHL 64
6/1/15 273 SEA ‑6
6/1/15 278 SEA ‑8
6/1/15 292 EWR 12
6/1/15 300 HNL 20
6/1/15 317 IND ‑10
... (13815 rows omitted)
One flight departed 16 minutes early, and one was 580 minutes late. The other delay times were almost all between ‑10 minutes and 200 minutes, as
the histogram below shows.
united.column('Delay').min()

-16

united.column('Delay').max()

580

delay_bins = np.append(np.arange(-20, 301, 10), 600)

united.hist('Delay', bins = delay_bins, unit = 'minute')

For the purposes of this section, it is enough to zoom in on the bulk of the data and ignore the 0.8% of flights that had delays of more than 200
minutes. This restriction is just for visual convenience; the table still retains all the data.
united.where('Delay', are.above(200)).num_rows/united.num_rows

0.008390596745027125

delay_bins = np.arange(-20, 201, 10)

united.hist('Delay', bins = delay_bins, unit = 'minute')

The height of the [0, 10) bar is just under 3% per minute, which means that just under 30% of the flights had delays between 0 and 10 minutes. That
is confirmed by counting rows:
united.where('Delay', are.between(0, 10)).num_rows/united.num_rows

0.2935985533453888

10.2.1. Empirical Distribution of the Sample

Let us now think of the 13,825 flights as a population, and draw random samples from it with replacement. It is helpful to package our code into a
function. The function empirical_hist_delay takes the sample size as its argument and draws an empiricial histogram of the results.
def empirical_hist_delay(n):
united.sample(n).hist('Delay', bins = delay_bins, unit = 'minute')

As we saw with the dice, as the sample size increases, the empirical histogram of the sample more closely resembles the histogram of the population.
Compare these histograms to the population histogram above.
empirical_hist_delay(10)

empirical_hist_delay(100)
The most consistently visible discrepancies are among the values that are rare in the population. In our example, those values are in the the right
hand tail of the distribution. But as the sample size increases, even those values begin to appear in the sample in roughly the correct proportions.
empirical_hist_delay(1000)

10.2.2. Convergence of the Empirical Histogram of the Sample

What we have observed in this section can be summarized as follows:
For a large random sample, the empirical histogram of the sample resembles the histogram of the population, with high probability.
This justifies the use of large random samples in statistical inference. The idea is that since a large random sample is likely to resemble the population
from which it is drawn, quantities computed from the values in the sample are likely to be close to the corresponding quantities in the population.

10.3. Empirical Distribution of a Statistic

The Law of Averages implies that with high probability, the empirical distribution of a large random sample will resemble the distribution of the
population from which the sample was drawn.
The resemblance is visible in two histograms: the empirical histogram of a large random sample is likely to resemble the histogram of the population.
As a reminder, here is the histogram of the delays of all the flights in united, and an empirical histogram of the delays of a random sample of 1,000 of
these flights.
united = Table.read_table(path_data + 'united_summer2015.csv')

delay_bins = np.arange(-20, 201, 10)

united.hist('Delay', bins = delay_bins, unit = 'minute')
plots.title('Population');
sample_1000 = united.sample(1000)
sample_1000.hist('Delay', bins = delay_bins, unit = 'minute')
plots.title('Sample of Size 1000');

The two histograms clearly resemble each other, though they are not identical.

10.3.1. Parameter
Frequently, we are interested in numerical quantities associated with a population.
In a population of voters, what percent will vote for Candidate A?
In a population of Facebook users, what is the largest number of Facebook friends that the users have?
In a population of United flights, what is the median departure delay?
Numerical quantities associated with a population are called parameters. For the population of flights in united, we know the value of the parameter
“median delay”:
np.median(united.column('Delay'))

2.0

The NumPy function median returns the median (half‑way point) of an array. Among all the flights in united, the median delay was 2 minutes. That is,
about 50% of flights in the population had delays of 2 or fewer minutes:
united.where('Delay', are.below_or_equal_to(2)).num_rows / united.num_rows

0.5018444846292948

Half of all flights left no more than 2 minutes after their scheduled departure time. That’s a very short delay!
Note. The percent isn’t exactly 50 because of “ties,” that is, flights that had delays of exactly 2 minutes. There were 480 such flights. Ties are quite
common in data sets, and we will not worry about them in this course.
united.where('Delay', are.equal_to(2)).num_rows

480

10.3.2. Statistic
In many situations, we will be interested in figuring out the value of an unknown parameter. For this, we will rely on data from a large random sample
drawn from the population.
A statistic (note the singular!) is any number computed using the data in a sample. The sample median, therefore, is a statistic.
Remember that sample_1000 contains a random sample of 1000 flights from united. The observed value of the sample median is:
np.median(sample_1000.column('Delay'))

2.0

Our sample – one set of 1,000 flights – gave us one observed value of the statistic. This raises an important problem of inference:
The statistic could have been different. A fundamental consideration in using any statistic based on a random sample is that the sample could
have come out differently, and therefore the statistic could have come out differently too.
np.median(united.sample(1000).column('Delay'))

3.0

Run the cell above a few times to see how the answer varies. Often it is equal to 2, the same value as the population parameter. But sometimes it is
different.
Just how different could the statistic have been? One way to answer this is to simulate the statistic many times and note the values. A histogram
of those values will tell us about the distribution of the statistic.
Let’s recall the main steps in a simulation.

10.3.3. Simulating a Statistic

We will simulate the sample median using the steps we set up in an earlier chapter when we started studying simulation. You can replace the sample
size of 1000 by any other sample size, and the sample median by any other statistic.
Step 1: Decide which statistic to simulate. We have already decided that: we are going to simulate the median of a random sample of size 1000
drawn from the population of flight delays.
Step 2: Define a function that returns one simulated value of the statistic. Draw a random sample of size 1000 and compute the median of the
sample. We did this in the code cell above. Here it is again, encapsulated in a function.
def random_sample_median():
return np.median(united.sample(1000).column('Delay'))

Step 3: Decide how many simulated values to generate. Let’s do 5,000 repetitions.
Step 4: Use a for loop to generate an array of simulated values. As usual, we will start by creating an empty array in which to collect our results.
We will then set up a for loop for generating all the simulated values. The body of the loop will consist of generating one simulated value of the
sample median, and appending it to our collection array.
The simulation takes a noticeable amount of time to run. That is because it is performing 5000 repetitions of the process of drawing a sample of size
1000 and computing its median. That’s a lot of sampling and repeating!
medians = make_array()

for i in np.arange(5000):
medians = np.append(medians, random_sample_median())

The simulation is done. All 5,000 simulated sample medians have been collected in the array medians. Now it’s time to visualize the results.

10.3.4. Visualization
Here are the simulated random sample medians displayed in the table simulated_medians.
simulated_medians = Table().with_column('Sample Median', medians)
simulated_medians

Sample Median
2
3
1
3
2
2.5
3
3
3
2
... (4990 rows omitted)
We can also visualize the simulated data using a histogram. The histogram is called an empirical histogram of the statistic. It displays the empirical
distribution of the statistic. Remember that empirical means observed.
simulated_medians.hist(bins=np.arange(0.5, 5, 1))

You can see that the sample median is very likely to be about 2, which was the value of the population median. Since samples of 1000 flight delays
are likely to resemble the population of delays, it is not surprising that the median delays of those samples should be close to the median delay in the
population.
This is an example of how a statistic can provide a good estimate of a parameter.

10.3.5. The Power of Simulation

If we could generate all possible random samples of size 1000, we would know all possible values of the statistic (the sample median), as well as the
probabilities of all those values. We could visualize all the values and probabilities in the probability histogram of the statistic.
But in many situations including this one, the number of all possible samples is large enough to exceed the capacity of the computer, and purely
mathematical calculations of the probabilities can be intractably difficult.
This is where empirical histograms come in.
We know that by the Law of Averages, the empirical histogram of the statistic is likely to resemble the probability histogram of the statistic, if the
sample size is large and if you repeat the random sampling process numerous times.
This means that simulating random processes repeatedly is a way of approximating probability distributions without figuring out the probabilities
mathematically or generating all possible random samples. Thus computer simulations become a powerful tool in data science. They can help data
scientists understand the properties of random quantities that would be complicated to analyze in other ways.

10.4. Random Sampling in Python

This section summarizes the ways you have learned to sample at random using Python, and introduces a new way.

10.4.1. Review: Sampling from a Population in a Table

If you are sampling from a population of individuals whose data are represented in the rows of a table, then you can use the Table method sample to
randomly select rows of the table. That is, you can use sample to select a random sample of individuals.
By default, sample draws uniformly at random with replacement. This is a natural model for chance experiments such as rolling a die.
faces = np.arange(1, 7)
die = Table().with_columns('Face', faces)
die

Face
1
2
3
4
5
6
Run the cell below to simulate 7 rolls of a die.
die.sample(7)

Face
5
3
3
5
5
1
6
Sometimes it is more natural to sample individuals at random without replacement. This is called a simple random sample. The argument
with_replacement=False allows you to do this.

actors = Table.read_table(path_data + 'actors.csv')

actors
Actor Total Number of Average per #1 Movie Gross
Gross Movies Movie
Harrison Ford 4871.7 41 118.8 Star Wars: The Force 936.7
Awakens
Samuel L. 4772.8 69 69.2 The Avengers 623.4
Jackson
Morgan
Freeman 4468.3 61 73.3 The Dark Knight 534.9
Tom Hanks 4340.8 44 98.7 Toy Story 3 415
Robert
Downey, Jr. 3947.3 53 74.5 The Avengers 623.4
Eddie Murphy 3810.4 38 100.3 Shrek 2 441.2
Tom Cruise 3587.2 36 99.6 War of the Worlds 234.3
Johnny Depp 3368.6 45 74.9 Dead Man's Chest 423.3
Michael Caine 3351.5 58 57.8 The Dark Knight 534.9
Scarlett
Johansson 3341.2 37 90.3 The Avengers 623.4
... (40 rows omitted)
# Simple random sample of 5 rows
actors.sample(5, with_replacement=False)

Actor Total Number of Average per #1 Movie Gross

Gross Movies Movie
Morgan
Freeman 4468.3 61 73.3 The Dark Knight 534.9
Orlando Bloom 2815.8 17 165.6 Dead Man's 423.3
Chest
Cameron Diaz 3031.7 34 89.2 Shrek 2 441.2
Michael Caine 3351.5 58 57.8 The Dark Knight 534.9
Leonardo 2518.3 25 100.7 Titanic 658.7
DiCaprio
Since sample gives you the entire sample in the order in which the rows were selected, you can use Table methods on the sampled table to answer
many questions about the sample. For example, you can find the number of times the die showed six spots, or the average number of movies in
which the sampled actors appeared, or whether one two specified actors appeared in the sample. You might need multiple lines of code to get some
of this information.

10.4.2. Review: Sampling from a Population in an Array

If you are sampling from a population of individuals whose data are represented as an array, you can use the NumPy function np.random.choice to
randomly select elements of the array.
By default, np.random.choice samples at random with replacement.
# The faces of a die, as an array
faces

array([1, 2, 3, 4, 5, 6])

# 7 rolls of the die

np.random.choice(faces, 7)

array([4, 1, 6, 3, 5, 4, 6])

The argument replace=False allows you to get a simple random sample, that is, a sample drawn at random without replacement.
# Array of actor names
actor_names = actors.column('Actor')

# Simple random sample of 5 actor names

np.random.choice(actor_names, 5, replace=False)

array(['Jonah Hill', 'Julia Roberts', 'Bruce Willis', 'Eddie Murphy',

'Matt Damon'], dtype='<U22')

Just as sample did, so also np.random.choice gives you the entire sequence of sampled elements. You can use array operations to answer many
questions about the sample. For example, you can find which actor was the second one to be drawn, or the number of faces of the die that appeared
more than once. Some answers might need multiple lines of code.

10.4.3. Sampling from a Categorical Distribution

Sometimes we are interested in a categorical attribute of our sampled individuals. For example, we might be looking at whether a coin lands Heads or
Tails. Or we might be interested in the political parties of randomly selected voters.
In such cases, we frequently need the proportions of sampled voters in the different categories. If we have the entire sample, we can calculate these
proportions. The function sample_proportions in the datascience library does that work for us. It is tailored for sampling at random with
replacement from a categorical distribution and returns the proportions of sampled elements in each category.
The sample_proportions function takes two arguments:
the sample size
the distribution of the categories in the population, as a list or array of proportions that add up to 1
It returns an array containing the distribution of the categories in a random sample of the given size taken from the population. That’s an array
consisting of the sample proportions in all the different categories, in the same order in which they appeared in the population distribution.
For example, suppose each plant of a species is red‑flowering with chance 25%, pink‑flowering with chance 50%, and white‑flowering with chance
25%, regardless of the flower colors of all other plants. You can use sample_proportions to see the proportions of the different colors among 300
plants of the species.
# Species distribution of flower colors:
# Proportions are in the order Red, Pink, White
species_proportions = [0.25, 0.5, .25]

sample_size = 300

# Distribution of sample
sample_distribution = sample_proportions(sample_size, species_proportions)
sample_distribution

array([0.24333333, 0.50333333, 0.25333333])

As you expect, the proportions in the sample sum to 1.

sum(sample_distribution)

1.0

The categories in species_proportions are in the order Red, Pink, White. That order is preserved by sample_proportions. If you just want the
proportion of pink‑flowering plants in the sample, you can use item:
# Sample proportion of Heads
sample_distribution.item(1)

0.5033333333333333
You can use sample_proportions and array operations to answer questions based only on the proportions of sampled individuals in the different
categories. You will not be able to answer questions that require more detailed information about the sample, such as which of the sampled plants
had each of the different colors.

11. Testing Hypotheses

Data scientists are often faced with yes‑no questions about the world. You have seen some examples of such questions in this course:
Is chocolate good for you?
Did water from the Broad Street pump cause cholera?
Have the demographics in California changed over the past decade?
Whether we answer questions like these depends on the data we have. Census data about California can settle questions about demographics with
hardly any uncertainty about the answer. We know that Broad Street pump water was contaminated by waste from cholera victims, so we can make a
pretty good guess about whether it caused cholera.
Whether chocolate or any other treatment is good for you will almost certainly have to be decided by medical experts, but an initial step consists of
using data science to analyze data from studies and randomized experiments.
In this chapter, we will try to answer such yes‑no questions, basing our conclusions on random samples and empirical distributions.

11.1. Assessing a Model

In data science, a model is a set of assumptions about data. Often, models include assumptions about chance processes used to generate data.
Sometimes, data scientists have to decide whether or not a model is good. In this section we will discuss an example of making such a decision.

11.1.1. Jury Selection

Data science can be a powerful tool for exposing racism and inequality in our society. This section is about a case where data provided evidence of
racial bias in jury selection.
Amendment VI of the United States Constitution states that, “In all criminal prosecutions, the accused shall enjoy the right to a speedy and public
trial, by an impartial jury of the State and district wherein the crime shall have been committed.”
One characteristic of an impartial jury is that it should be selected from a jury panel that is representative of the population of the relevant region. A
jury panel is a group of people chosen to be prospective jurors. The final trial jury is selected from among them by deliberate inclusion or exclusion,
and as a result can have any composition. But the larger panel from which the trial jurors are drawn must be representative of the population.
The question of whether a jury panel is indeed representative of a region’s population has an important legal implication. If some group in the
population was systematically underrepresented on the jury panel, that could raise a question about whether the jury was impartial and hence
whether the defendant received due process.
That was the question in the Supreme Court case of Robert Swain, a Black man convicted in Talladega County, Alabama, in 1962. He appealed his
indictment all the way to the U.S. Supreme Court on the grounds that Black people were systematically excluded from juries in Talladega County. The
Supreme Court denied his appeal and Robert Swain was later sentenced to life imprisonment.
However, our analysis below shows that the data are not in agreement with conclusions drawn by the Court. On the contrary, the data point to bias in
the jury selection process. This bias in the criminal justice system reflected the widespread prejudice and injustice prevalent against Black people at
the time.
We will start by looking at the numerical details. At the time of the trial, only men aged 21 or more were eligible to serve on juries in Talladega County.
In that population, 26% of the men were Black. As is common in jury trials, the jurors in the trial of Robert Swain were selected from a panel of people
who were supposed to be representative of the population of eligible jurors. But only eight men among the panel of 100 men (that is, 8%) were Black.
As part of his appeal, Robert Swain questioned this discrepancy. Moreover, he pointed out that all Talladega County jury panels for the past 10 years
had contained only a small percent of Black panelists.
The U.S. Supreme Court reviewed the appeal and concluded, “the overall percentage disparity has been small.” But was this assertion reasonable? If
jury panelists were selected at random from the county’s eligible population, there would be some chance variation. We wouldn’t get exactly 26 Black
panelists on every 100‑person panel. But would we expect as few as eight?
The answer is no. We will establish that and then discuss some of the many biases involved.

11.1.2. A Model of Random Selection

One view of the data – a model, in other words – is that the panel was selected at random and ended up with a small number of Black panelists just
due to chance.
Since the panel was supposed to resemble the population of all eligible jurors, the model of random selection is important to assess. Let’s see if it
stands up to scrutiny.
The model specifies the details of a chance process. It says the data are like a random sample from a population in which 26% of the people are
Black. We are in a good position to assess this model for the following reasons.
We can simulate data based on the model. That is, we can simulate drawing at random from a population of whom 26% are Black.
Our simulation will show what a panel would be like if it were selected at random.
We can then compare the results of the simulation with the composition of an actual jury panel.
If the results of our simulation are not consistent with the composition of the panel in the trial, that will be evidence against the model of random
selection. Therefore, it will be evidence against the fairness of the trial.
Let’s go through the process step by step.

11.1.3. The Statistic

First, we have to choose a statistic to simulate. The statistic has to be able to help us decide between the model and alternative views about the data.
The model says the panel was drawn at random from the eligible population. The alternative viewpoint is the case for Robert Swain, which is that the
panel contained too few Black panelists to have been drawn at random. A natural statistic, then, is the number or count of Black panelists in the
sample. Small values of the statistic will favor Robert Swain’s viewpoint.

11.1.4. Simulating the Statistic Under the Model

If the model were true, how big would the statistic typically be? To answer that, will simulate the statistic under the assumption of random selection
and look at the distribution of the results.

11.1.4.1. Simulating One Value of the Statistic

We can use sample_proportions to simulate one value of the statistic. The sample size is 100, the size of the panel. The distribution from which we
will sample is the distribution in the population of eligible jurors. Since 26% of them were Black, we will sample from the distribution specified by the
proportions [0.26, 0.74].
sample_size = 100
eligible_population = [0.26, 0.74]

The categories in the output array of sample_proportions are in the same order as in the input array. So the proportion of Black panelists in the
random sample is item(0) of the output array. Run the cell below a few times to see how the sample proportion of Black jurors varies in a randomly
selected panel. Do you see any values as low as 0.08?
sample_proportions(sample_size, eligible_population).item(0)

0.27

The count in each category is the sample size times the corresponding proportion. So we can just as easily simulate counts instead of proportions.
Let’s define a function that does this. The function will draw a panel at random and return the number of panelists who are Black.
def one_simulated_count():
return sample_size * sample_proportions(sample_size, eligible_population).item(0)

11.1.4.2. Simulating Multiple Values of the Statistic

The focus of our analysis is the variability in the counts. Let’s generate 10,000 simulated values of the count and see how they vary. As usual, we will
do this by using a for loop and collecting all the simulated counts in an array.
counts = make_array()
repetitions = 10000
for i in np.arange(repetitions):
counts = np.append(counts, one_simulated_count())

11.1.5. The Prediction Under the Model of Random Selection

To interpret the results of our simulation, we can visualize the results in an empirical histogram of the simulated counts.
Table().with_column(
'Count in a Random Sample', counts
).hist(bins = np.arange(5.5, 46.6, 1))

The histogram shows us what the model of random selection predicts about our statistic, the number of Black panelists in the sample.
To generate each simulated count, we drew 100 times at random from a population in which 26% were Black. So, as you would expect, most of the
simulated counts are around 26. They are not exactly 26: there is some variation. The counts range from about 15 to about 40.

11.1.6. Comparing the Prediction and the Data

In the panel selected for the trial, there were eight Black panelists. The histogram of simulated counts is redrawn below with value eight shown as a
red dot on the horizontal axis. The dot is very far out in the left hand tail of the histogram. Very few of the 10,000 counts simulated by random
selection came out to be eight or less.
Table().with_column(
'Count in a Random Sample', counts
).hist(bins = np.arange(5.5, 46.6, 1))
plots.ylim(-0.002, 0.09)
plots.scatter(8, 0, color='red', s=30);
11.1.7. Conclusion of the Data Analysis
The graph above is a visual display of bias in the selection process. It shows that if we select a panel of size 100 at random from the eligible
population, we are very unlikely to get counts of Black panelists that are as low as the eight that were observed on the panel in the trial.
This is evidence that the model of random selection of the jurors in the panel is not consistent with the data from the panel. While it is possible that
the panel could have been generated by chance, our simulation demonstrates that it is hugely unlikely.
The reality of the trial panel is very much at odds with the model’s assumption of random selection from the eligible population. When the data and a
model are inconsistent, the model is hard to justify. After all, the data are real. The model is just a set of assumptions. When assumptions are at odds
with reality, we must question those assumptions.
Therefore the most reasonable conclusion is that the assumption of random selection is unjustified for this jury panel. In other words, the most
reasonable conclusion is that the jury panel was not selected by random sampling from the population of eligible jurors. Notwithstanding the opinion
of the Supreme Court, the difference between 26% and 8% is not so small as to be explained well by chance alone.

11.1.8. Statistical Bias

The analysis above provides quantitative evidence of unfairness in Robert Swain’s trial. The data support his position that he was denied the impartial
jury to which he was entitled by the U.S. Constitution.
Additional data show that the exclusion of Black panelists was pervasive. The Supreme Court judgment, written in 1965, includes evidence provided
by Robert Swain that “only 10 to 15% of … jury panels drawn from the jury box since 1953 have been [Black], there having been only one case in
which the percentage was as high as 23%.” Look at where 10% and 15% lie on the horizontal axis of the histogram above. Values like that are also
highly unlikely under random selection from the eligible population.
When a process produces errors that are systematically in one direction – such as the percentage of Black panelists always being lower than
expected – then data scientists say the process is biased. Quantification of such bias is an important responsibility of data science.
Arguments such as the one in this section are now more frequently presented in courts of law. In the 1960s, the Supreme Court looked at the data
but drew the wrong conclusion that “the overall percentage disparity has been small.” For the meaning of “small,” it was wrong to rely on what simply
seemed reasonable to the majority of the Court. Views on what was reasonable were not only purely subjective, they were also vulnerable to the
influence of pervasive racial prejudice. If arguments in the case had included the quantitative analysis of this section, the Court might not have
concluded that the percentage disparity was small.

11.1.9. Racial Bias

The statistical bias in the selection process was born out of deep‑seated racial bias in the legal system of the time.
For example, the Supreme Court judgment says that Talladega County jury panels were selected from a jury roll of names that the jury commissioners
acquired from “city directories, registration lists, club and church lists, conversations with other persons in the community, both white and [not
white], and personal and business acquaintances.” This process was clearly biased against Black people and in favor of people in the commissioners’
social and professional circles. Such systematic exclusion of Black people from the jury rolls meant that very few Black people were selected for the
jury panels.
Even when there were Black panelists, they typically did not make it into the final jury. Of the eight Black men on Robert Swain’s jury panel, two were
excused and six were eliminated by the prosecution in a process called a peremptory challenge. In this process, lawyers for both sides could exclude
or strike a certain number of panelists without giving a reason.
Arguing against the unfairness of peremptory challenges was a significant part of Robert Swain’s appeal. He noted that “prosecutors have
consistently and systematically exercised their strikes to prevent any and all [Black panelists] from serving on the [jury] itself.” The Court
acknowledged that there had never been a Black juror in any civil or criminal case in Talladega County. But it still denied the appeal.
Racial bias in the legal system derived from bias in society. Prejudice and injustice against Black people had been so prevalent for so long that in
many parts of society it had become almost a normal way to think and act. As members of society, the Justices of the Supreme Court were not
immune to this. The Court majority presented their decision as the most appropriate and logical interpretation of the law. But it was not. The Court’s
decision on peremptory challenges was eventually reversed after legal battles that lasted 20 years.
Robert Swain fought a criminal justice system that was stacked against him. Here, we have been able to expose just one aspect of the systemic bias
and racism that he faced and that so many other Black people have fought against. For many, the fight continues to this day. We believe that data
science can be a powerful ally.

11.1.10. Further Reading

Robert Swain was represented in the U.S. Supreme Court by Constance Baker Motley, the first African‑American woman to argue a case in that
Court. She argued 10 cases in the Supreme Court and lost only one – Robert Swain’s case in 1965.
Thurgood Marshall, who in 1967 became the first African‑American Supreme Court Justice, had studied the Court’s decision in Robert Swain’s case
and pressed for eliminating peremptory challenges that were based on race alone. This was achieved in the 1986 Supreme Court case Batson v.
Kentucky.
But Marshall had concerns about the efficacy of the Batson decision. He anticipated that some legal teams would circumvent it by finding ostensibly
race‑neutral ways to exclude Black jurors. In his opinion concurring with the majority of the Court, he recommended going further and banning
peremptory challenges altogether. His concluding words were, “I applaud the Court’s holding that the racially discriminatory use of peremptory
challenges violates the Equal Protection Clause, and I join the Court’s opinion. However, only by banning peremptories entirely can such
discrimination be ended.” Thurgood Marshall’s concerns were prescient, as you will see in some of the readings below.
In 2013, Constance Baker Motley was posthumously awarded a Congressional gold medal “in recognition of her enduring contributions and service to
the United States.” In support of the award, members of the House of Representatives wrote, “Constance Baker Motley’s only loss before the United
States Supreme Court was in Swain v. Alabama, 380 U.S. 202 (1965), a case in which the Court refused to proscribe race‑based peremptory
challenges in cases involving African‑American defendants and which was later reversed in Batson v. Kentucky, 476 U.S. 79 (1986), on grounds that
had been largely asserted by Constance Baker Motley in the Swain case.”
Thurgood Marshall and Constance Baker Motley had other connections. For example, as a student at Columbia Law School, Baker Motley worked as
a law clerk for Marshall. Some years later she wrote the original complaint in the landmark civil rights case Brown v. Board of Education in Topeka,
which was won by Thurgood Marshall in 1954.
The NAACP Legal Defense and Educational Fund argued Robert Swain’s case and later supported the Batson case.
In spite of the Batson decision, racial bias in jury selection persists. Legal scholar and Berkeley Law School alum Richard L. Harris Jr. has provided a
detailed account of the biases that are perpetuated by peremptory challenges.
In their 2020 report Whitewashing the Jury Box: How California Perpetuates the Discriminatory Exclusion of Black and Latinx Jurors, Professor
Elisabeth Semel and co‑authors in the Berkeley Law Death Penalty Clinic describe how Thurgood Marshall’s concerns about the effectiveness of the
Batson ruling are justified by experience in Californian courts.
The U.S. Supreme Court judgment in the case Swain v. Alabama can be distressing to read. We have included it because some excerpts are quoted in
the section.

11.2. Multiple Categories

Whether jury panels are representative of the eligible population continues to be an important question. We will address it in the context of more
recent panels than that of Robert Swain in the 1960s.
The general process of assessment will be the same as before. But this time we will consider panelists in multiple racial and ethnic categories, not
just two. From a technical perspective, this will mean that we have to come up with a new statistic to simulate. Once we have simulated it and arrived
at a conclusion, we will examine some of the underlying causes of the discrepancies that we observe.

11.2.1. Jury Selection in Alameda County

In 2010, the American Civil Liberties Union (ACLU) of Northern California presented a report on jury selection in Alameda County, California. The
report concluded that certain racial and ethnic groups are underrepresented among jury panelists in Alameda County, and suggested some reforms
of the process by which eligible jurors are assigned to panels. In this section, we will analyze the data provided by the ACLU.
As you saw in the previous section, trial jurors are selected from a larger jury panel. By law, the jury panel is supposed to be representative of the
population of eligible jurors. In California, the word “representative” is clearly defined as “selected at random.” Section 197 of California’s Code of Civil
Procedure says, “All persons selected for jury service shall be selected at random, from a source or sources inclusive of a representative cross
section of the population of the area served by the court.”
Here “selected for jury service” means being selected to be on the jury panel.

11.2.2. Composition of Panels in Alameda County

The focus of the study by the ACLU of Northern California was the racial and ethnic composition of jury panels in Alameda County. The ACLU
compiled data on the composition of the jury panels in 11 felony trials in Alameda County in the years 2009 and 2010. In those panels, the total
number of people who reported for jury service was 1453. The ACLU gathered demographic data on all of these prosepctive jurors, and compared
those data with the composition of all eligible jurors in the county.
The data are tabulated below in a table called jury. In each category, the first numerical value is the proportion of all eligible juror candidates in that
category. The second value is the proportion of people in that category among those who appeared for the process of selection into the jury.
The labels for the different categories are taken from the ACLU report, which says, “The category “other” includes people who identified as mixed
race without identifying one primary racial identity, and individuals who did not identify a race or ethnicity.” The label Asian/PI means “Asian or
Pacific Islander.” The label Black/AA means “Black or African‑American.”
jury = Table().with_columns(
'Ethnicity', make_array('Asian/PI', 'Black/AA', 'Caucasian', 'Hispanic', 'Other'),
'Eligible', make_array(0.15, 0.18, 0.54, 0.12, 0.01),
'Panels', make_array(0.26, 0.08, 0.54, 0.08, 0.04)
)

jury

Ethnicity Eligible Panels

Asian/PI 0.15 0.26
Black/AA 0.18 0.08
Caucasian 0.54 0.54
Hispanic 0.12 0.08
Other 0.01 0.04
Some ethnicities are overrepresented and some are underrepresented on the jury panels in the study. In particular, panelists in the Black/AA and
Hispanic categories are underrepresented.
A bar chart is helpful for visualizing the differences.
jury.barh('Ethnicity')
11.2.3. Comparison with Panels Selected at Random
What if we select a random sample of 1,453 people from the population of eligible jurors? Will the distribution of their ethnicities look like the
distribution of the panels above?
We can answer these questions by using sample_proportions and augmenting the jury table with a column of the proportions in our sample.
Technical note. Random samples of prospective jurors would be selected without replacement. However, when the size of a sample is small relative
to the size of the population, sampling without replacement resembles sampling with replacement; the proportions in the population don’t change
much between draws. The population of eligible jurors in Alameda County is over a million, and compared to that, a sample size of about 1500 is quite
small. We will therefore sample with replacement.
In the cell below, we sample at random 1453 times from the distribution of eligible jurors, and display the distribution of the random sample along with
the distributions of the eligible jurors and the panel in the data.
eligible_population = jury.column('Eligible')
sample_distribution = sample_proportions(1453, eligible_population)
panels_and_sample = jury.with_column('Random Sample', sample_distribution)
panels_and_sample

Ethnicity Eligible Panels Random Sample

Asian/PI 0.15 0.26 0.14384
Black/AA 0.18 0.08 0.163799
Caucasian 0.54 0.54 0.538197
Hispanic 0.12 0.08 0.143152
Other 0.01 0.04 0.0110117
The distribution of the random sample is quite close to the distribution of the eligible population, unlike the distribution of the panels. As always, it
helps to visualize.
panels_and_sample.barh('Ethnicity')

The bar chart shows that the distribution of the random sample resembles the eligible population but the distribution of the panels does not.
To assess whether this observation is particular to one random sample or more general, we can simulate multiple panels under the model of random
selection and see what the simulations predict. But we won’t be able to look at thousands of bar charts like the one above. We need a statistic that
will help us assess whether or not the model or random selection is supported by the data.

11.2.4. A New Statistic: The Distance between Two Distributions

We know how to measure how different two numbers are: if the numbers are $x$ and $y$, the distance between them is $\vert x‑y \vert$. Now we
have to quantify the distance between two distributions. For example, we have to measure the distance between the blue and gold distributions
below.
jury.barh('Ethnicity')

For this we will compute a quantity called the total variation distance between two distributions. The calculation is as an extension of how we find the
distance between two numbers.
To compute the total variation distance, we first find the difference between the two proportions in each category.
# Augment the table with a column of differences between proportions

jury_with_diffs = jury.with_column(
'Difference', jury.column('Panels') - jury.column('Eligible')
)
jury_with_diffs

Ethnicity Eligible Panels Difference

Asian/PI 0.15 0.26 0.11
Black/AA 0.18 0.08 ‑0.1
Caucasian 0.54 0.54 0
Hispanic 0.12 0.08 ‑0.04
Other 0.01 0.04 0.03
Take a look at the column Difference and notice that the sum of its entries is 0: the positive entries add up to 0.14, exactly canceling the total of the
negative entries which is ‑0.14.
This is numerical evidence of the fact that in the bar chart, the gold bars exceed the blue bars by exactly as much as the blue bars exceed the gold.
The proportions in each of the two columns Panels and Eligible add up to 1, and so the give‑and‑take between their entries must add up to 0.
To avoid the cancellation, we drop the negative signs and then add all the entries. But this gives us two times the total of the positive entries
(equivalently, two times the total of the negative entries, with the sign removed). We don’t need that doubling, so we divide the sum by 2.
jury_with_diffs = jury_with_diffs.with_column(
'Absolute Difference', np.abs(jury_with_diffs.column('Difference'))
)

jury_with_diffs
Ethnicity Eligible Panels Difference Absolute Difference
Asian/PI 0.15 0.26 0.11 0.11
Black/AA 0.18 0.08 ‑0.1 0.1
Caucasian 0.54 0.54 0 0
Hispanic 0.12 0.08 ‑0.04 0.04
Other 0.01 0.04 0.03 0.03
jury_with_diffs.column('Absolute Difference').sum() / 2

0.14

This quantity 0.14 is the total variation distance (TVD) between the distribution of ethnicities in the eligible juror population and the distribution in the
panels.
In general, the total variation distance between two distributions measures how close the distributions are. The larger the TVD, the more different the
two distributions appear.
Technical Note: We could have obtained the same result by just adding the positive differences. But our method of including all the absolute
differences eliminates the need to keep track of which differences are positive and which are not.
We will use the total variation distance between distributions as the statistic to simulate under the assumption of random selection. Large values of
the distance will be evidence against random selection.

11.2.5. Simulating the Statistic Under the Model

To see how the TVD varies across random samples, we will simulate it repeatedly under the model of random selection from the eligible population.
Let’s organize our calculation. Since we are going to be computing total variation distance repeatedly, we will first write a function that computes it for
two given distributions.
The function total_variation_distance takes two arrays containing the distributions to compare, and returns the TVD between them.
def total_variation_distance(distribution_1, distribution_2):
return sum(np.abs(distribution_1 - distribution_2)) / 2

This function will help us calculate our statistic in each repetition of the simulation. But first let’s check that it gives the right answer when we use it to
compute the distance between the blue (eligible) and gold (panels) distributions above. These are the distribution in the ACLU study.
total_variation_distance(jury.column('Panels'), jury.column('Eligible'))

0.14

This agrees with the value that we computed directly without using the function.
In the cell below we use the function to compute the TVD between the distributions of the eligible jurors and one random sample. Recall that
eligible_population is the array containing the distribution of the eligible jurors, and that our sample size is 1453.

In the first line, we use sample_proportions to generate a random sample from the eligible population. In the next line we use
total_variation_distance to compute the TVD between the distributions in the random sample and the eligible population.

sample_distribution = sample_proportions(1453, eligible_population)

total_variation_distance(sample_distribution, eligible_population)

0.018265657260839632

Run the cell a few times and notice that the distances are quite a bit smaller than 0.14, the distance between the distribution of the panels and the
eligible jurors.
We are now ready to run a simulation to assess the model of random selection.

11.2.5.1. Simulating One Value of the Statistic

In the same way that we start every simulation, let’s define a function one_simulated_tvd that returns one simulated value of the total variation
distance under the hypothesis of random selection.
The code in the body of the definition is based on the cell above.
# Simulate one simulated value of
# the total variation distance between
# the distribution of a sample selected at random
# and the distribution of the eligible population

def one_simulated_tvd():
sample_distribution = sample_proportions(1453, eligible_population)
return total_variation_distance(sample_distribution, eligible_population)

11.2.5.2. Simulating Multiple Values of the Statistic

Now we can apply the familiar process of using a for loop to create an array consisting of 5000 such distances.
tvds = make_array()
repetitions = 5000
for i in np.arange(repetitions):
tvds = np.append(tvds, one_simulated_tvd())

11.2.6. Assessing the Model of Random Selection

Here is the empirical histogram of the simulated distances. It shows that if you draw 1453 panelists at random from the pool of eligible candidates,
then the distance between the distributions of the panelists and the eligible population is rarely more than about 0.05.
The panels in the study, however, were not quite so similar to the eligible population. The total variation distance between the panels and the
population was 0.14, shown as the red dot on the horizontal axis. It is far beyond the tail of the histogram and does not look at all like a typical
distance between the distributions of a random sample and the eligible population.
Table().with_column('TVD', tvds).hist(bins=np.arange(0, 0.2, 0.005))

# Plotting parameters; you can ignore this code

plots.title('Prediction Assuming Random Selection')
plots.xlim(0, 0.15)
plots.ylim(-5, 50)
plots.scatter(0.14, 0, color='red', s=30);

The simulation shows that the composition of the panels in the ACLU study is not consistent with the model of random selection. Our analysis
supports the ACLU’s conclusion that the panels were not representative of the distribution provided for the eligible jurors.

11.2.7. Reasons for the Bias

As with most such analyses, ours doesn’t say why the distributions are different. But those reasons are important to understand. If jury panels don’t
represent the population of eligible jurors, that can have a major effect on due process and the fairness of jury trials.
The ACLU report discusses several possible reasons for the discrepancies and suggests some remedies. Some are purely practical but have a big
impact. For example, while we can take for granted the high quality of random sampling in Python, the panel selection used other software. The
ACLU’s examination revealed that the software didn’t work well, contributing to biased selection. Using better software is a clear remedy.
More significantly, Alameda County jury panels are not selected from the entire eligible population. The website of the Superior Court of Alameda
County says, “The objective of the court is to provide an accurate cross‑section of the county’s population. The names of jurors are selected at
random from everyone who is a registered voter and/or has a driver’s license or identification card issued by the Department of Motor Vehicles.”
This process excludes eligible jurors who are not on those lists. Having state‑issued ID or being registered to vote is most likely associated with
income and hence also with race and ethnicity due to historical bias against Black and Hispanic communities. This leads to underrepresentation of
those groups on the panels.
Those on the list have to be reached in order to inform them of their jury summons. But people in under‑resourced communities don’t always have
fixed addresses. Out‑of‑date address records, lack of cross‑checking with other lists such as those of the utilities, and so on can all contribute to
biased selection.
Once reached, the potential panelists still have to be able to appear. The first day of jury service is not compensated, and compensation for
subsequent days is $15 per day. While employers are required by law to excuse employees who have jury duty, they are not required to provide
compensation, and some employers don’t. In a region as expensive as the Bay Area, this can become a reason for panelists not to respond to jury
summons. Though jurors can be excused for severe economic hardship, even the process of requesting to be excused can be out of reach for some
jurors. Across the Bay, city leaders in San Francisco are attempting to reduce this form of bias by piloting a program that provides compensation of
$100 per day to low‑income jurors.

11.2.8. Data Quality

We have developed a technique that helps us decide whether one distribution looks like a random sample from another. But we should examine our
data sources to better understand exactly what we can conclude from our analysis. Good data science includes a thoughtful examination of how the
data were gathered.
Eligible Jurors. It is important to keep in mind that not everyone is eligible to serve on a jury. On its website, the Superior Court of Alameda County
says, “You may be called to serve if you are 18 years old, a U.S. citizen and a resident of the county or district where summoned. You must be able to
understand English, and be physically and mentally capable of serving. In addition, you must not have served as any kind of juror in the past 12
months, nor have been convicted of a felony.”
Though the Census is a natural source of demographic information, the Census doesn’t collect data on all these categories. Thus the ACLU had to
obtain the demographics of eligible jurors in some other way.
What they used was a set of estimates that had been developed by a San Diego State University professor for an Alameda County trial in 2002.
Those estimates were based on the 2000 Census and also took into account the criteria required for eligibility as a juror.
So we have to keep in mind that the distribution that we used for the eligible population is itself an estimate and is therefore subject to error.
Moreover, as the ACLU noted, using estimates based on the 2000 Census for populations in 2010 might not be accurate due to the changing
demographics in California.
Thus the distribution used for the population of eligible jurors might not be accurate.
Panels. It is not clear from the report exactly how the 1453 panelists were classified into the different ethnic categories. The report says only that
“attorneys … cooperated in collecting jury pool data”.
Significant social, cultural, and political factors affect who gets classified or self‑classifies into each ethnic category. It is also not clear if the
definitions of those categories in the panels were the same as those used in the estimates of the distribution of eligible jurors. This raises questions
about the correspondence between the two distributions being compared.
Moreover, the data on panelists was obtained from those who reported for service. As we have discussed, not all panelists do so. The reasons for not
reporting are associated with race and ethnicity, and disproportionately affect panelists from under‑resourced communities.
Responding to jury summons is required by law. But as the ACLU noted, at the time of the study Alameda County did not have an effective process
for following up on prospective jurors who had been called but had failed to appear. The ACLU recommended the creation of “a failure to appear
program that requires, at a minimum, the issuance of a second notice to prospective jurors.”
Indeed, following up on non‑respondents would reduce bias. For our analysis, we must acknowledge that we don’t have the data needed to fill in the
demographic information for panelists who were selected but did not report for service.

11.2.9. Conclusion
Because of the discussion above, it is important for us to be precise about what we can conclude from our analysis.
We can conclude that the distribution provided for the panelists who reported for service does not look like a random sample from the
estimated distribution in the eligible population.
Our discussion, like the discussion in the ACLU report, sets out reasons for some of the differences observed between the two distributions and for
why summoned panelists might nor report. Almost all the reasons have their roots in historical racial bias in society, and are examples of the lasting
negative consequences of that bias.

11.3. Decisions and Uncertainty

The statistical and computational methodology that we developed for assessing models about jury selection fit into a general framework of decision
making called statistical tests of hypotheses. Using statistical tests as a way of making decisions is standard in many fields and has a standard
terminology.
In this section we will describe the general sequence of the steps used in statistical tests, along with some terminology.
Though our example is from the biological sciences, you will see that the statistical and computational steps in the process are consistent with the
corresponding steps in our analyses of data from the legal system. However, the biological data are about plants, not human beings and injustice. So
the context and interpretation of the calculations below are far more simple.
Gregor Mendel (1822‑1884) was an Austrian monk who is widely recognized as the founder of the modern field of genetics. Mendel performed
careful and large‑scale experiments on plants to come up with fundamental laws of genetics.
Many of his experiments were on varieties of pea plants. He formulated sets of assumptions about each variety; these were his models. He then
tested the validity of his models by growing the plants and gathering data.
For pea plants of a particular variety, Mendel proposed the following model.

11.3.1. Mendel’s Model

For every plant, there is a 75% chance that it will have purple flowers, and a 25% chance that the flowers will be white, regardless of the colors in all
the other plants.
To see whether his model was valid, Mendel grew 929 pea plants of this variety. Among these 929 plants, 705 had purple flowers.
We will use these data to perform a test of hypotheses and see if Mendel’s model looks good.

11.3.2. Step 1: The Hypotheses

All statistical tests attempt to choose between two views of the world. Specifically, the choice is between two views about how the data were
generated. These two views are called hypotheses.
The null hypothesis. This is a clearly defined model about chances. It says that the data were generated at random under clearly specified
assumptions about the randomness. The word “null” reinforces the idea that if the data look different from what the null hypothesis predicts, the
difference is due to nothing but chance.
From a practical perspective, the null hypothesis is a hypothesis under which you can simulate data.
In the example about Mendel’s model for the colors of pea plants, the null hypothesis is that the assumptions of his model are good: each plant has a
75% chance of having purple flowers, independent of all other plants.
Under this hypothesis, we can simulate random samples by using sample_proportions.
The alternative hypothesis. This says that some reason other than chance made the data differ from the predictions of the model in the null
hypothesis.
In the example about Mendel’s plants, the alternative hypothesis is simply that his model isn’t good.
Keep in mind that the alternative doesn’t say how or why the model isn’t good. It just says the model isn’t good.

11.3.3. Step 2: The Test Statistic

In order to decide between the two hypothesis, we must choose a statistic that we can use to make the decision. This is called the test statistic.
We will be comparing two categorical distributions: the one in Mendel’s model and the one we will get in our random sample. We want to see if these
two distributions are close to each other or far apart. So a natural test statistic is the total variation distance (TVD) developed in the previous section.
It turns out that with just two categories, the TVD is rather simple and easy to interpret. Let’s look at an example. Mendel’s model says that the
“purple, white” distribution is [0.75, 0.25]. Suppose the distribution in our sample came out to be [0.7, 0.3].
Because there are only two categories, something interesting happens when we calculate the TVD. First notice that
\[ \vert 0.7 ‑ 0.75 \vert = 0.05 = \vert 0.3 ‑ 0.25 \vert \]
So the TVD is
\[ \frac{1}{2}\big{(} \vert 0.7 ‑ 0.75 \vert + \vert 0.3 ‑ 0.25 \vert \big{)} = 0.05 = \vert 0.7 ‑ 0.75 \vert \]
That’s just the distance between the two proportions of purple‑flowering plants. It is also just the distance between the two proportions of white‑
flowering plants.
By a bit of math that we won’t do here, this is true whenever there are just two categories: the TVD is equal to the distance between the two
proportions in one category.
So a perfectly fine test statistic would be the distance between the sample proportion of purple plants and 0.75 which is the corresponding
proportion in Mendel’s model.
Since percents are easier to interpret than proportions, we will work with percents instead.
Our test statistic will be the distance between the sample percent of purple plants and 75% which is the corresponding percent in Mendel’s model.
\[ \big{\vert} \text{sample percent of purple‑flowering plants} ‑ 75 \big{\vert} \]
This test statistic is a distance between the two distributions. It makes sense and is easy to use. A sample percent of around 75% will be consistent
with the model, but percents much bigger or much less than 75 will make you think that the model isn’t good. Therefore, small values of the distance
will make you lean towards the null hypothesis. Big values of the statistic will make you lean towards the alternative.
To choose a test statistic in other situations, look at the alternative hypothesis. What values of the statistic will make you think that the alternative
hypothesis is a better choice than the null?
If the answer is “big values,” you have a good choice of statistic.
So also if the answer is “small values.”
But if the answer is “both big values and small values,” we recommend that you look again at your statistic. See if using a distance instead of a
difference can change the answer to just “big values”.

11.3.3.1. Observed Value of the Test Statistic

The observed value of the test statistic is the value of the statistic you get from the data in the study, not a simulated value. Among Mendel’s 929
plants, 705 had purple flowers. The observed value of the test statistic was therefore
observed_statistic = abs ( 100 * (705 / 929) - 75)
observed_statistic

0.8880516684607045

11.3.4. Step 3: The Distribution of the Test Statistic, Under the Null Hypothesis
The main computational aspect of a test of hypotheses is figuring out what the model in the null hypothesis predicts. Specifically, we have to figure
out what the values of the test statistic might be if the null hypothesis were true.
The test statistic is simulated based on the assumptions of the model in the null hypothesis. That model involves chance, so the statistic comes out
differently when you simulate it multiple times.
By simulating the statistic repeatedly, we get a good sense of its possible values and which ones are more likely than others. In other words, we get a
good approximation to the probability distribution of the statistic, as predicted by the model in the null hypothesis.
As with all distributions, it is very useful to visualize this distribution by a histogram, as we have done in our previous examples. Let’s go through the
entire process here.
We will start by assigning some known quantities to names.
mendel_proportions = make_array(0.75, 0.25)
mendel_proportion_purple = mendel_proportions.item(0)
sample_size = 929

Next, we will define a function that returns one simulated value of the test statistic. Then we will use a for loop to collect 10,000 simulated values in
an array.
def one_simulated_distance():
sample_proportion_purple = sample_proportions(929, mendel_proportions).item(0)
return 100 * abs(sample_proportion_purple - mendel_proportion_purple)

repetitions = 10000
distances = make_array()
for i in np.arange(repetitions):
distances = np.append(distances, one_simulated_distance())

Now we can draw the histogram of these values. This is the histogram of the distribution of the test statistic predicted by the null hypothesis.
Table().with_column(
'Distance between Sample % and 75%', distances
).hist()
plots.title('Prediction Made by the Null Hypothesis');

Look on the horizontal axis to see the typical values of the distance, as predicted by the model. They are rather small. For example, a high proportion
of the distances are in the range 0 to 1, meaning that for a high proportion of the samples, the percent of purple‑flowering plants is in the range 75% \
(\pm\) 1%. That is, the sample percent is in the range 74% to 76%.
Also note that this prediction was made using Mendel’s model only, not the proportions observed by Mendel in the plants that he grew. It is time now
to compare the predictions and Mendel’s observation.

11.3.5. Step 4. The Conclusion of the Test

The choice between the null and alternative hypotheses depends on the comparison between what you computed in Steps 2 and 3: the observed
value of the test statistic and its distribution as predicted by the null hypothesis.
If the two are not consistent with each other, then the data do not support the null hypothesis. In other words, the alternative hypothesis is better
supported by the data. We say that the test rejects the null hypothesis.
If the two are consistent with each other, then the observed test statistic is in line with what the null hypothesis predicts. In other words, the null
hypothesis is better supported by the data. We say that the data are consistent with the null hypothesis.
In our example, the observed value of the test statistic is about 0.89, as computed in Step 2 above. Just by eye, locate roughly where 0.89 is on the
horizontal axis of the histogram. You will see that it is clearly in the heart of the distribution predicted by Mendel’s model.
The cell below redraws the histogram with the observed value plotted on the horizontal axis.
Table().with_column(
'Distance between Sample % and 75%', distances
).hist()
plots.ylim(-0.02, 0.5)
plots.title('Prediction Made by the Null Hypothesis')
plots.scatter(observed_statistic, 0, color='red', s=40);

The observed statistic is like a typical distance predicted by the null hypothesis. The null hypothesis is Mendel’s model. So our test concludes that
the data are consistent with Mendel’s model.
Based on our data, Mendel’s model looks good.

11.3.6. The Meaning of “Consistent”

In all of our examples of assessing models there has been no doubt about whether the data were consistent with the model’s predictions. They were
either very far from what the model predicted, as in the examples about jury panels, or similar to what the model predicted, as in the example about
Mendel’s model.
But outcomes are not always so clear cut. How far is “far”? Exactly what should “similar” mean? While these questions don’t have universal answers,
there are some guidelines and conventions that you can follow.
But first, it is important to understand that whether the observed test statistic is consistent with its predicted distribution under the null hypothesis is
a matter of subjective opinion and judgment. We recommend that you provide your judgment along with the value of the test statistic and a graph of
its predicted distribution under the null. That will allow your readers to make their own judgment about whether the two are consistent.
In the example above, the judgment is clear. But suppose someone grew another 929 plants of some related variety and wanted to see if Mendel’s
model worked for plants of that variety too. What would you conclude if their observed distance came out to be 3.2 as shown below?
different_observed_statistic = 3.2
Table().with_column(
'Distance between Sample % and 75%', distances
).hist()
plots.ylim(-0.02, 0.5)
plots.title('Prediction Made by the Null Hypothesis')
plots.scatter(different_observed_statistic, 0, color='red', s=40);
Is the observation based on the new variety of plants consistent with the predictions in the histogram, or not?
Now the answer is not so clear. It depends on whether you think the red dot is too far from the bulk of the predicted values to be consistent with the
prediction based on Mendel’s model.

11.3.7. Conventional Cut‑offs and the P‑value

If you don’t want to use your own judgment, there are conventions that you can follow. These conventions tell us how far out into the tails is
conventionally considered “too far”.
The conventions are based on the area in the tail, starting at the observed statistic (the red dot) and looking in the direction that makes us lean
toward the alternative. In this example that’s the right side, because big distances favor the alternative which says that the model isn’t good.
If the area of the tail is small, the observed statistic is far away from the values most commonly predicted by the null hypothesis.
Remember that in a histogram, area represents percent. To find the area in the tail, we have to find the percent of distances that were greater than or
equal to 3.2, where the red dot is. The array distances contains the averages for all 10,000 repetitions of random sampling under Mendel’s model,
and different_observed_statistic is 3.2.
np.count_nonzero(distances >= different_observed_statistic) / repetitions

0.0243

About 2.4% of the distances simulated under Mendel’s model were 3.2 or greater. By the law of averages, we can conclude that if Mendel’s model
were correct for these new plants, then there is about a 2.4% chance that the test statistic would be 3.2 or more.
That doesn’t seem like a big chance. If Mendel’s model is true for these plants, something quite unlikely has happened. This idea gives rise to the
conventions.

11.3.7.1. The p‑Value

This chance has an impressive name. It is called the observed significance level of the test. That’s a mouthful, and so it is commonly called the p‑
value of the test.
Definition: The p‑value of a test is the chance, based on the model in the null hypothesis, that the test statistic will be equal to the observed value in
the sample or even further in the direction that supports the alternative.
If a p‑value is small, that means the tail beyond the observed statistic is small and so the observed statistic is far away from what the null predicts.
This implies that the data support the alternative hypothesis more than they support the null.
How small is “small”? According to the conventions:
If the p‑value is less than 5%, it is considered small and the result is called “statistically significant.”
If the p‑value is even smaller – less than 1% – the result is called “highly statistically significant.”
By this convention, our p‑value of 2.4% is considered small. So the conventional conclusion would be to reject the null hypothesis and say that
Mendel’s model does not look good for the new plants. Formally, the result of the test is statistically significant.
When you make a conclusion in this way, we recommend that you don’t just say whether or not the result is statistically significant. Along with your
conclusion, provide the observed statistic and the p‑value as well, so that readers can use their own judgment.

11.3.8. Historical Note on the Conventions

The determination of statistical significance, as defined above, has become standard in statistical analyses in all fields of application. When a
convention is so universally followed, it is interesting to examine how it arose.
The method of statistical testing – choosing between hypotheses based on data in random samples – was developed by Sir Ronald Fisher in the early
20th century. Sir Ronald might have set the convention for statistical significance somewhat unwittingly, in the following statement in his 1925 book
Statistical Methods for Research Workers. About the 5% level, he wrote, “It is convenient to take this point as a limit in judging whether a deviation is
to be considered significant or not.”
What was “convenient” for Sir Ronald became a cutoff that has acquired the status of a universal constant. No matter that Sir Ronald himself made
the point that the value was his personal choice from among many: in an article in 1926, he wrote, “If one in twenty does not seem high enough odds,
we may, if we prefer it draw the line at one in fifty (the 2 percent point), or one in a hundred (the 1 percent point). Personally, the author prefers to set
a low standard of significance at the 5 percent point …”
Fisher knew that “low” is a matter of judgment and has no unique definition. We suggest that you too keep this in mind. Provide your data, make your
judgment, and explain why you made it.
Whether you use a conventional cutoff or your own judgment, it is important to keep the following points in mind.
Always provide the observed value of the test statistic and the p‑value, so that readers can decide whether or not they think the p‑value is
small.
Don’t look to defy convention only when the conventionally derived result is not to your liking.
Even if a test concludes that the data don’t support the chance model in the null hypothesis, it typically doesn’t explain why the model doesn’t
work. Don’t make causal conclusions without further analysis, unless you are running a randomized controlled trial. We will analyze those in a
later section.

11.4. Error Probabilities

In the process by which we decide which of two hypotheses is better supported by our data, the final step involves a judgment about the consistency
of the data and the null hypothesis. While this step results in a good decision a vast majority of the time, it can sometimes lead us astray. The reason
is chance variation. For example, even when the null hypothesis is true, chance variation might cause the sample to look quite different from what the
null hypothesis predicts.

11.4.1. Wrong Conclusions

If you are testing a null hypothesis against the alternative that the null hypothesis isn’t true, then there are four ways of classifying reality and the
result of the test.
Test Favors the Null Test Favors the Alternative
Null is True Correct result Error
Alternative is True Error Correct result
In two out of the four cells of this table, the test result is wrong. One type of error occurs if the test favors the alternative hypothesis when in fact the
null hypothesis is true. The other type of error occurs if the test favors the null hypothesis when in fact the alternative hypothesis is true.
Since the null hypothesis is a completely specified chance model, the first type of error has a chance that we can estimate. The answer turns out to
be essentially the cutoff that we use for the p‑value. Let’s see how.

11.4.2. The Chance of an Error

Suppose you want to test whether a coin is fair or not. Then the hypotheses are:
Null: The coin is fair. That is, the results are like draws made at random with replacement from Heads, Tails.
Alternative: The coin is not fair.
Suppose you are going to test this hypothesis based on 2000 tosses of the coin. You would expect a fair coin to land heads 1000 times out of 2000,
so a reasonable test statistic to use is
\[ \text{test statistic} ~ = ~ \big{\vert} ~ \text{number of heads} ‑ 1000 ~ \big{\vert} \]
Small values of this statistic favor the null hypothesis, and large values favor the alternative.
We have simulated this statistic under the null hypothesis many times, and drawn its empirical distribution.

The area to the right of 45, colored gold, is just under 5%.
np.count_nonzero(statistics >= 45) / repetitions

0.04654

Large values of the test statistic favor the alternative. So if you wanted to use a 5% cutoff for the p‑value, your decision rule would be to conclude
that the coin is unfair if the test statistic comes out to be 45 or more.
However, as the figure shows, a fair coin can produce test statistics with values 45 or more. In fact it does so with chance approximately 5%.
Summary: If the coin is fair and our test uses a 5% cutoff for deciding whether it is fair or not, then there is about a 5% chance that the test will
wrongly conclude that the coin is unfair.

11.4.3. The Cutoff for the p‑value is an Error Probability

The example above is a special case of a general fact:
If you use a $p$% cutoff for the p‑value, and the null hypothesis happens to be true, then there is about a $p$% chance that your test will
conclude that the alternative is true.
Here is the table of the four possible reality/test outcomes again. Probabilities in the top row are computed under the assumption that the null
hypothesis is true. The p‑value is the probability of the error shown in red.
Test Favors the Null Test Favors the Alternative
Null is True Correct result Error
Alternative is True Error Correct result

11.4.3.1. Controlling for the Error

The 1% cutoff is therefore more conservative than 5%. With the 1% cutoff there is less chance of concluding “alternative” if the null happens to be
true. For this reason, randomized controlled trials of medical treatments usually use 1% as the cutoff for deciding between the following two
hypotheses:
Null: The treatment has no effect; the observed differences between the outcomes of the treatment and control groups of patients are due to
randomization.
Alternative: The treatment has an effect.
The idea is to control the chance of concluding that the treatment does something if in fact it does nothing. This reduces the risk of giving patients a
useless treatment.
Still, even if you set the cutoff to be as low as 1%, and the treatment does nothing, there is about a 1% chance of concluding that the treatment does
something. This is due to chance variation. There is a small chance that data from random samples end up leading you astray. The advantage of
random sampling is that you can find that chance.

11.4.4. Data Snooping and p‑Hacking

The discussion above implies that if each of 100 different research groups runs a separate randomized controlled experiment about the effect of a
treatment that in fact has no effect, and each experiment uses a 1% cutoff for the p‑value, then by chance variation, one of the experiments is
expected to wrongly conclude that the treatment does have an effect.
Unfortunately, that could be the one that gets published. This is why it is important that experiments be replicated. That is, other researchers ought
to be able to carry out the experiment and see if they get similar results.
It is not uncommon for researchers to test multiple hypotheses using the same data. For example, in a randomized controlled trial about the effect of
a drug, researchers might test whether the drug has an effect on various different diseases.
Now suppose the drug has no effect on anything. Just by chance variation, a small percent of the tests might conclude that it does have an effect.
So, when you read a study that uses tests of hypotheses and concludes that a treatment has an effect, always ask how many different effects were
tested before the researchers found the one that was reported.
If the researchers ran multiple different tests before finding one that gave a “highly statistically significant” result, use the result with caution. The
study could be marred by data snooping, which essentially means torturing the data into making a false confession. This is sometimes also called p‑
hacking.
In such a situation, one way to validate the reported result is by replicating the experiment and testing for that particular effect alone. If it comes out
significant again, that will validate the original conclusion.

11.4.5. Technical Note: The Other Kind of Error

There is, of course, another kind of error: concluding that the treatment does nothing when in fact it does something. Discussions of that error are
outside the scope of this course. Just be aware that life isn’t easy: if you set up your test to reduce one of the two errors, you almost always increase
the other one.

12. Comparing Two Samples

We have seen several examples of assessing whether a single sample looks like random draws from a specified chance model.
Did the Alameda County jury panels look like a random sample from the population of eligible jurors?
Did the pea plants that Mendel grew have colors that were consistent with the chances he specified in his model?
In all of these cases there was just one random sample, and we were trying to decide how it had been generated. But often, data scientists have to
compare two random samples with each other. For example, they might have to compare the outcomes of patients who have been assigned at
random to a treatment group and a control group. Or they might have randomized internet users to receive two different versions of a website, after
which they would want to compare the actions of the two random groups.
In this chapter, we develop a way of using Python to compare two random samples and answer questions about the similarities and differences
between them. You will see that the methods we develop have diverse applications. Our examples are from medicine and public health as well as
football!

12.1. A/B Testing

In modern data analytics, deciding whether two numerical samples come from the same underlying distribution is called A/B testing. The name refers
to the labels of the two samples, A and B.
We will develop the method in the context of an example. The data come from a sample of newborns in a large hospital system. We will treat it as if it
were a simple random sample though the sampling was done in multiple stages. Stat Labs by Deborah Nolan and Terry Speed has details about a
larger dataset from which this set is drawn.

12.1.1. Smokers and Nonsmokers

The table births contains the following variables for 1,174 mother‑baby pairs: the baby’s birth weight in ounces, the number of gestational days, the
mother’s age in completed years, the mother’s height in inches, pregnancy weight in pounds, and whether or not the mother smoked during
pregnancy.
births = Table.read_table(path_data + 'baby.csv')
births

Birth Gestational Maternal Maternal Maternal Pregnancy Maternal

Weight Days Age Height Weight Smoker
120 284 27 62 100 False
113 282 33 64 135 False
128 279 28 64 115 True
108 282 23 67 125 True
136 286 25 62 93 False
138 244 33 62 178 False
132 245 23 65 140 False
120 289 25 62 125 False
143 299 30 66 136 True
140 351 27 68 120 False
... (1164 rows omitted)
One of the aims of the study was to see whether maternal smoking was associated with birth weight. Let’s see what we can say about the two
variables.
We’ll start by selecting just Birth Weight and Maternal Smoker. There are 715 non‑smokers among the women in the sample, and 459 smokers.
smoking_and_birthweight = births.select('Maternal Smoker', 'Birth Weight')

smoking_and_birthweight.group('Maternal Smoker')

Maternal Smoker count

False 715
True 459
Let’s look at the distribution of the birth weights of the babies of the non‑smoking mothers compared to those of the smoking mothers. To generate
two overlaid histograms, we will use hist with the optional group argument which is a column label or index. The rows of the table are first grouped
by this column and then a histogram is drawn for each one.
smoking_and_birthweight.hist('Birth Weight', group = 'Maternal Smoker')
The distribution of the weights of the babies born to mothers who smoked appears to be based slightly to the left of the distribution corresponding to
non‑smoking mothers. The weights of the babies of the mothers who smoked seem lower on average than the weights of the babies of the non‑
smokers.
This raises the question of whether the difference reflects just chance variation or a difference in the distributions in the larger population. Could it be
that there is no difference between the two distributions in the population, but we are seeing a difference in the samples just because of the mothers
who happened to be selected?

12.1.2. The Hypotheses

We can try to answer this question by a test of hypotheses. The chance model that we will test says that there is no underlying difference in the
populations; the distributions in the samples are different just due to chance.
Formally, this is the null hypothesis. We are going to have to figure out how to simulate a useful statistic under this hypothesis. But as a start, let’s just
state the two natural hypotheses.
Null hypothesis: In the population, the distribution of birth weights of babies is the same for mothers who don’t smoke as for mothers who do. The
difference in the sample is due to chance.
Alternative hypothesis: In the population, the babies of the mothers who smoke have a lower birth weight, on average, than the babies of the non‑
smokers.

12.1.3. Test Statistic

The alternative hypothesis compares the average birth weights of the two groups and says that the average for the mothers who smoke is smaller.
Therefore it is reasonable for us to use the difference between the two group means as our statistic.
We will do the subtraction in the order “average weight of the smoking group $‑$ average weight of the non‑smoking group”. Small values (that is,
large negative values) of this statistic will favor the alternative hypothesis.
The observed value of the test statistic is about $‑9.27$ ounces.
means_table = smoking_and_birthweight.group('Maternal Smoker', np.average)
means_table

Maternal Smoker Birth Weight average

False 123.085
True 113.819
means = means_table.column(1)
observed_difference = means.item(1) - means.item(0)
observed_difference

-9.266142572024918

We are going compute such differences repeatedly in our simulations below, so we will define a function to do the job. The function takes two
arguments:
the name of the table of data
the label of the column that contains the Boolean variable for grouping
It returns the difference between the means of the True group and the False group.
You will soon see why we are specifying the two arguments. For now, just check that the function returns what it should.
def difference_of_means(table, group_label):
"""Takes: name of table,
column label that indicates the group to which the row belongs
Returns: Difference of mean birth weights of the two groups"""
reduced = table.select('Birth Weight', group_label)
means_table = reduced.group(group_label, np.average)
means = means_table.column(1)
return means.item(1) - means.item(0)

To check that the function is working, let’s use it to calculate the observed difference between the mean birth weights of the two groups in the
sample.
difference_of_means(births, 'Maternal Smoker')

-9.266142572024918

That’s the same as the value of observed_difference calculated earlier.

12.1.4. Predicting the Statistic Under the Null Hypothesis

To see how the statistic should vary under the null hypothesis, we have to figure out how to simulate the statistic under that hypothesis. A clever
method based on random permutations does just that.
If there were no difference between the two distributions in the underlying population, then whether a birth weight has the label True or False with
respect to maternal smoking should make no difference to the average. The idea, then, is to shuffle all the labels randomly among the mothers. This
is called random permutation.
Shuffling ensures that the count of True labels does not change, and nor does the count of False labels. This is important for the comparability of the
simulated differences of means and the original difference of means. We will see later in the course that the sample size affects the variability of a
sample mean.
Take the difference of the two new group means: the mean weight of the babies whose mothers have been randomly labeled smokers and the mean
weight of the babies of the remaining mothers who have all been randomly labeled non‑smokers. This is a simulated value of the test statistic under
the null hypothesis.
Let’s see how to do this. It’s always a good idea to start with the data. We have reduced the table to have just the columns that we need.
smoking_and_birthweight

Maternal Smoker Birth Weight

False 120
False 113
True 128
True 108
False 136
False 138
False 132
False 120
True 143
False 140
... (1164 rows omitted)
There are 1,174 rows in the table. To shuffle all the labels, we will draw a random sample of 1,174 rows without replacement. Then the sample will
include all the rows of the table, in random order.
We can use the Table method sample with the optional with_replacement=False argument. We don’t have to specify a sample size, because by
default, sample draws as many times as there are rows in the table.
shuffled_labels = smoking_and_birthweight.sample(with_replacement = False).column(0)
original_and_shuffled = smoking_and_birthweight.with_column('Shuffled Label',
shuffled_labels)

original_and_shuffled

Maternal Smoker Birth Weight Shuffled Label

False 120 True
False 113 False
True 128 False
True 108 True
False 136 False
False 138 False
False 132 True
False 120 False
True 143 True
False 140 False
... (1164 rows omitted)
Each baby’s mother now has a random smoker/non‑smoker label in the column Shuffled Label, while her original label is in Maternal Smoker. If the
null hypothesis is true, all the random re‑arrangements of the labels should be equally likely.
Let’s see how different the average weights are in the two randomly labeled groups.
shuffled_only = original_and_shuffled.select('Birth Weight','Shuffled Label')
shuffled_group_means = shuffled_only.group('Shuffled Label', np.average)
shuffled_group_means

Shuffled Label Birth Weight average

False 119.277
True 119.752
The averages of the two randomly selected groups are quite a bit closer than the averages of the two original groups. We can use our function
difference_of_means to find the two differences.

difference_of_means(original_and_shuffled, 'Shuffled Label')

0.4747109100050153

difference_of_means(original_and_shuffled, 'Maternal Smoker')

-9.266142572024918

But could a different shuffle have resulted in a larger difference between the group averages? To get a sense of the variability, we must simulate the
difference many times.
As always, we will start by defining a function that simulates one value of the test statistic under the null hypothesis. This is just a matter of collecting
the code that we wrote above.
The function is called one_simulated_difference_of_means. It takes no arguments, and returns the difference between the mean birth weights of
two groups formed by randomly shuffling all the labels.
def one_simulated_difference_of_means():
"""Returns: Difference between mean birthweights
of babies of smokers and non-smokers after shuffling labels"""

# array of shuffled labels

shuffled_labels = births.sample(with_replacement=False).column('Maternal Smoker')

# table of birth weights and shuffled labels

shuffled_table = births.select('Birth Weight').with_column(
'Shuffled Label', shuffled_labels)

return difference_of_means(shuffled_table, 'Shuffled Label')

Run the cell below a few times to see how the output changes.
one_simulated_difference_of_means()

-0.058299434770034964

12.1.5. Permutation Test

Tests based on random permutations of the data are called permutation tests. We are performing one in this example. In the cell below, we will
simulate our test statistic – the difference between the average birth weight of the two randomly formed groups – many times and collect the
differences in an array.
differences = make_array()

repetitions = 5000
for i in np.arange(repetitions):
new_difference = one_simulated_difference_of_means()
differences = np.append(differences, new_difference)

The array differences contains 5,000 simulated values of our test statistic: the difference between the mean weight in the smoking group and the
mean weight in the non‑smoking group, when the labels have been assigned at random.

12.1.6. Conclusion of the Test

The histogram below shows the distribution of these 5,000 values. It is the empirical distribution of the test statistic simulated under the null
hypothesis. This is a prediction about the test statistic, based on the null hypothesis.
Table().with_column('Difference Between Group Means', differences).hist()
print('Observed Difference:', observed_difference)
plots.title('Prediction Under the Null Hypothesis');

Observed Difference: -9.266142572024918

Notice how the distribution is centered roughly around 0. This makes sense, because under the null hypothesis the two groups should have roughly
the same average. Therefore the difference between the group averages should be around 0.
The observed difference in the original sample is about $‑9.27$ ounces, which doesn’t even appear on the horizontal scale of the histogram. The
observed value of the statistic and the predicted behavior of the statistic under the null hypothesis are inconsistent.
The conclusion of the test is that the data favor the alternative over the null. It supports the hypothesis that the average birth weight of babies born to
mothers who smoke is less than the average birth weight of babies born to non‑smokers.
If you want to compute an empirical p‑value, remember that low values of the statistic favor the alternative hypothesis.
empirical_p = np.count_nonzero(differences <= observed_difference) / repetitions
empirical_p

0.0

The empirical p‑value is 0, meaning that none of the 5,000 permuted samples resulted in a difference of ‑9.27 or lower. This is only an approximation.
The exact chance of getting a difference in that range is not 0. But it is vanishingly small, according to our simulation, and therefore we can reject the
null hypothesis.

12.1.7. Another Permutation Test

We can use the same method to compare other attributes of the smokers and the non‑smokers, such as their ages. Histograms of the ages of the
two groups show that in the sample, the mothers who smoked tended to be younger.
smoking_and_age = births.select('Maternal Smoker', 'Maternal Age')
smoking_and_age.hist('Maternal Age', group = 'Maternal Smoker')

The observed difference between the average ages is about $‑0.8$ years.
Let’s rewrite the code that compared the birth weights so that it now compares the ages of the smokers and non‑smokers.
def difference_of_means(table, group_label):
"""Takes: name of table,
column label that indicates the group to which the row belongs
Returns: Difference of mean ages of the two groups"""
reduced = table.select('Maternal Age', group_label)
means_table = reduced.group(group_label, np.average)
means = means_table.column(1)
return means.item(1) - means.item(0)

observed_age_difference = difference_of_means(births, 'Maternal Smoker')

observed_age_difference

-0.8076725017901509

Remember that the difference is calculated as the mean age of the smokers minus the mean age of the non‑smokers. The negative sign shows that
the smokers are younger on average.
Is this difference due to chance, or does it reflect an underlying difference in the population?
As before, we can use a permutation test to answer this question. If the underlying distributions of ages in the two groups are the same, then the
empirical distribution of the difference based on permuted samples will predict how the statistic should vary due to chance.
We will follow the same process as in any simulation. We will start by writing a function that returns one simulated value of the difference between
means, and then write a for loop to simulate numerous such values and collect them in an array.
def one_simulated_difference_of_means():
"""Returns: Difference between mean ages
of smokers and non-smokers after shuffling labels"""

# array of shuffled labels

shuffled_labels = births.sample(with_replacement=False).column('Maternal Smoker')

# table of ages and shuffled labels

shuffled_table = births.select('Maternal Age').with_column(
'Shuffled Label', shuffled_labels)

return difference_of_means(shuffled_table, 'Shuffled Label')

age_differences = make_array()

repetitions = 5000
for i in np.arange(repetitions):
new_difference = one_simulated_difference_of_means()
age_differences = np.append(age_differences, new_difference)

The observed difference is in the tail of the empirical distribution of the differences simulated under the null hypothesis.
Table().with_column(
'Difference Between Group Means', age_differences).hist(
right_end = observed_age_difference)
# Plotting parameters; you can ignore the code below
plots.ylim(-0.1, 1.2)
plots.scatter(observed_age_difference, 0, color='red', s=40, zorder=3)
plots.title('Prediction Under the Null Hypothesis')
print('Observed Difference:', observed_age_difference)

Observed Difference: -0.8076725017901509

Once again, the empirical distribution of the simulated differences is centered roughly around 0, because the simulation is under the null hypothesis
that there is no difference between the distributions of the two groups.
The empirical p‑value of the test is the proportion of simulated differences that were equal to or less than the observed difference. This is because
low values of the difference favor the alternative hypothesis that the smokers were younger on average.
empirical_p = np.count_nonzero(age_differences <= observed_age_difference) / 5000
empirical_p

0.0108

The empirical p‑value is around 1% and therefore the result is statistically significant. The test supports the hypothesis that the smokers were
younger on average.

12.2. Causality
Our methods for comparing two samples have a powerful use in the analysis of randomized controlled experiments. Since the treatment and control
groups are assigned randomly in such experiements, differences in their outcomes can be compared to what would happen just due to chance if the
treatment had no effect at all. If the observed differences are more marked than what we would predict as purely due to chance, we will have
evidence of causation. Because of the unbiased assignment of individuals to the treatment and control groups, differences in the outcomes of the
two groups can be ascribed to the treatment.
The key to the analysis of randomized controlled experiments is understanding exactly how chance enters the picture. This helps us set up clear null
and alternative hypotheses. Once that’s done, we can simply use the methods of the previous sections to complete the analysis.
Let’s see how to do this in an example.

12.2.1. Treating Chronic Back Pain: A Randomized Controlled Trial

Low‑back pain in adults can be very persistent and hard to treat. Common methods run the gamut from corticosteroids to acupuncture. A
randomized controlled trial (RCT) examined the effect of using Botulinum Toxin A (BTA) as a treatment. Botulinum toxin is a neurotoxic protein that
causes the disease botulism; Wikipedia says that botulinum “is the most acutely lethal toxin known.” There are seven types of botulinum toxin.
Botulinum Toxin A is one of the types that can cause disease in humans, but it is also used in medicine to treat various diseases involving the
muscles. The RCT analyzed by Foster, Clapp, and Jabbari in 2001 examined it as a treatment for low back pain.
Thirty one patients with low‑back pain were randomized into treatment and control groups, with 15 in the treatment group and 16 in control. The
control group was given normal saline, and the trials were run double‑blind so that neither doctors nor patients knew which group they were in.
Eight weeks after the start of the study, nine of the 15 in the treatment group and two of the 16 in the control group had pain relief (according to a
precise definition used by the researchers). These data are in the table bta and appear to show that the treatment has a clear benefit.
bta = Table.read_table(path_data + 'bta.csv')
bta.show()
Group Result
Control 1
Control 1
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Control 0
Treatment 1
Treatment 1
Treatment 1
Treatment 1
Treatment 1
Treatment 1
Treatment 1
Treatment 1
Treatment 1
Treatment 0
Treatment 0
Treatment 0
Treatment 0
Treatment 0
Treatment 0
Let’s see how many patients recovered in each group. Remember that counting is the same as adding zeros and ones. The sum of 1’s in the control
group is the number of control group patients who had pain relief.
bta.group('Group', sum)

Group Result sum

Control 2
Treatment 9
Since counting is the same as the sum of zeros and ones, the proportion of patients who had pain relief is the average of zeros and ones. It is the sum
divided by the total number of patients in each group.
bta.group('Group', np.average)
Group Result average
Control 0.125
Treatment 0.6
In the treatment group, 60% of the patients had pain relief, compared to only 12.5% in the control group. None of the patients suffered any side
effects.
So the indications are that botulinum toxin A did better than the saline. But the conclusion isn’t yet a slam‑dunk. The patients were assigned at
random into the two groups, so perhaps the difference could just be due to chance?
To understand what this means, we have to consider the possibility that among the 31 patients in the study, some were simply better able to recover
than others, even without any help from the treatment. What if an unusually large proportion of such patients got assigned to the treatment group,
just by chance? Then even if the treatment did nothing more than the saline in the control group, the results of the treatment group might look better
than those of the control group.
To account for this possibility, let’s start by carefully setting up the chance model.

12.2.2. Potential Outcomes

Before the patients are randomized into the two groups, our minds instinctively imagine two possible outcomes for each patient: the outcome that the
patient would have if assigned to the treatment group, and the outcome that the same patient would have if assigned to the control group. These are
called the two potential outcomes of the patient.
Thus there are 31 potential treatment outcomes and 31 potential control outcomes. The question is about the distributions of these two sets of 31
outcomes each. Are they the same, or are they different?
We can’t answer this just yet, because we don’t get to see all 31 values in each group. We just get to see a randomly selected 16 of the potential
control outcomes, and the treatment outcomes of the remaining 15 patients.
Here is a good way to visualize the setting. Each patient has a two‑sided ticket:

After the randomization, we get to see the right half of a randomly selected set of tickets, and the left half of the remaining group.
The table observed_outcomes collects the information about every patient’s potential outcomes, leaving the unobserved half of each “ticket” blank.
(It’s just another way of thinking about the bta table, carrying the same information.)
observed_outcomes = Table.read_table(path_data + "observed_outcomes.csv")
observed_outcomes.show()
Group Outcome if assigned treatment Outcome if assigned control
Control Unknown 1
Control Unknown 1
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Control Unknown 0
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 1 Unknown
Treatment 0 Unknown
Treatment 0 Unknown
Treatment 0 Unknown
Treatment 0 Unknown
Treatment 0 Unknown
Treatment 0 Unknown

12.2.3. The Hypotheses

The question is whether the treatment does anything. In terms of the table observed_outcomes, the question is whether the distribution of the 31
“treatment” values in Column 1 (including the unknown ones) is different from the distribution of the 31 “control” values in Column 2 (again including
the unknown ones).
Null Hypothesis: The distribution of all 31 potential “treatment” outcomes is the same as that of all 31 potential “control” outcomes. Botulinum toxin
A does nothing different from saline; the difference in the two samples is just due to chance.
Alternative Hypothesis: The distribution of 31 potential “treatment” outcomes is different from that of the 31 control outcomes. The treatment does
something different from the control.
Notice that the alternative is not specifying that the treatment helps – just that it is different from the control. This is standard in medical studies
because it doesn’t pre‑judge which way the result might go. But you are welcome to run a test for whether the treatment does better than the
control. Just adjust your test statistic accordingly.
There are 31 observed outcomes jointly in the two groups. If the null hypothesis were true, it wouldn’t matter which of those 31 outcomes were
labeled “treatment” and which “control.” Any random subset of 16 out of the 31 values could be called “control” and the remaining 15 “treatment”.
We can simulate this. We can randomly permute the 31 values, split them into two groups of 16 and 15, and see how different the distributions in the
two groups are. Since the data are zeros and ones, we can just see how different the two proportions are.
That’s exactly what we did for A/B testing in the previous section. Sample A is now the control group and Sample B the treatment group. We will carry
out the test below showing the details of all the steps. You should confirm that they are the same as the steps carried out for A/B testing.

12.2.4. The Test Statistic

If the two group proportions are very different from each other, we will lean towards the alternative hypothesis that the two underlying distributions
are different. So our test statistic will be the distance between the two group proportions, that is, the absolute value of the difference between them.
Large values of the test statistic will favor the alternative hypothesis over the null.
Since the two group proportions were 0.6 and 0.125, the observed value of the test statistic is $\big{\vert} 0.6 ‑ 0.125 \big{\vert} = 0.475$.
bta.group('Group', np.average)

Group Result average

Control 0.125
Treatment 0.6
observed_proportions = bta.group('Group', np.average).column(1)
observed_distance = abs(observed_proportions.item(0) - observed_proportions.item(1))
observed_distance

0.475

As we have done before, we will define a function that takes the following two arguments:
the name of the table of data
the column label of the group labels
and returns the distance between the two group proportions.
def distance(table, group_label):
reduced = table.select('Result', group_label)
proportions = reduced.group(group_label, np.average).column(1)
return abs(proportions.item(1) - proportions.item(0))

distance(bta, 'Group')

0.475

12.2.5. Predicting the Statistic Under the Null Hypothesis

We can simulate results under the null hypothesis, to see how our test statistic should come out if the null hypothesis is true.

12.2.5.1. Generating One Value of the Statistic

The simulation follows exactly the same process we used in the previous section. We start by randomly permuting the all group labels and then
attaching the shuffled labels to the 0/1 results.
shuffled_labels = bta.sample(with_replacement=False).column(0)

bta_with_shuffled_labels = bta.with_column('Shuffled Label', shuffled_labels)

bta_with_shuffled_labels.show()
Group Result Shuffled Label
Control 1 Treatment
Control 1 Control
Control 0 Treatment
Control 0 Control
Control 0 Control
Control 0 Treatment
Control 0 Treatment
Control 0 Control
Control 0 Treatment
Control 0 Control
Control 0 Control
Control 0 Control
Control 0 Control
Control 0 Control
Control 0 Control
Control 0 Treatment
Treatment 1 Control
Treatment 1 Control
Treatment 1 Treatment
Treatment 1 Control
Treatment 1 Treatment
Treatment 1 Treatment
Treatment 1 Control
Treatment 1 Treatment
Treatment 1 Treatment
Treatment 0 Control
Treatment 0 Treatment
Treatment 0 Treatment
Treatment 0 Control
Treatment 0 Treatment
Treatment 0 Treatment
We can now find the distance between the two proportions after the group labels have been shuffled.
distance(bta_with_shuffled_labels, 'Shuffled Label')

0.08750000000000002

This is quite different from the distance between the two original proportions.
distance(bta_with_shuffled_labels, 'Group')

0.475

12.2.5.2. Permutation Test

If we shuffled the labels again, how different would the new distance be? To answer this, we will define a function that simulates one simulated value
of the distance under the hypothesis of random draws from the same underlying distribution. And then we will collect 20,000 such simulated values
in an array.
You can see that we are doing exactly what we did in our previous examples of the permutation test.
def one_simulated_distance():
shuffled_labels = bta.sample(with_replacement = False
).column('Group')
shuffled_table = bta.select('Result').with_column(
'Shuffled Label', shuffled_labels)
return distance(shuffled_table, 'Shuffled Label')

distances = make_array()

repetitions = 20000
for i in np.arange(repetitions):
new_distance = one_simulated_distance()
distances = np.append(distances, new_distance)

12.2.6. Conclusion of the Test

The array distances contains 20,000 values of our test statistic simulated under the null hypothesis. Here is their empirical histogram along with the
observed value of the statistic. To find the P‑value of the test, remember that large values of the distance favor the alternative hypothesis.
Table().with_column('Distance', distances).hist(
bins = np.arange(0, 0.7, 0.1), left_end = observed_distance)
# Plotting parameters; you can ignore the code below
plots.ylim(-0.1, 5.5)
plots.scatter(observed_distance, 0, color='red', s=40, zorder=3)
plots.title('Prediction Under the Null Hypothesis')
print('Observed Distance', observed_distance)

Observed Distance 0.475

To find the empirical p‑value numerically, we must find the proportion of simulated statistics that were equal to or larger than the observed statistic.
empirical_p = np.count_nonzero(distances >= observed_distance) / repetitions
empirical_p

0.00875

This is a small p‑value. The observed statistic is in the tail of the empirical histogram of the test statistic generated under the null hypothesis.
The result is statistically significant. The test favors the alternative hypothesis over the null. The evidence supports the hypothesis that the treatment
is doing something.
The study reports a P‑value of 0.009, or 0.9%, which is not far from our empirical value.

12.2.7. Causality
Because the trials were randomized, the test is evidence that the treatment causes the difference. The random assignment of patients to the two
groups ensures that there is no confounding variable that could affect the conclusion of causality.
If the treatment had not been randomly assigned, our test would still point toward an association between the treatment and back pain outcomes
among our 31 patients. But beware: without randomization, this association would not imply that the treatment caused a change in back pain
outcomes. For example, if the patients themselves had chosen whether to administer the treatment, perhaps the patients experiencing more pain
would be more likely to choose the treatment and more likely to experience some reduction in pain even without medication. Pre‑existing pain would
then be a confounding factor in the analysis.

12.2.8. A Meta‑Analysis
While the RCT does provide evidence that the botulinum toxin A treatment helped patients, a study of 31 patients isn’t enough to establish the
effectiveness of a medical treatment. This is not just because of the small sample size. Our results in this section are valid for the 31 patients in the
study, but we are really interested in the population of all possible patients.
In 2011, a group of researchers performed a meta‑analysis of the studies on the treatment. That is, they identified all the available studies of such
treatments for low‑back pain and summarized the collated results.
There were several studies but not many could be included in a scientifically sound manner: “We excluded evidence from nineteen studies due to
non‑randomisation, incomplete or unpublished data.” Only three randomized controlled trials remained, one of which is the one we have studied in
this section. The meta‑analysis gave it the highest assessment among all the studies (LBP stands for low‑back pain): “We identified three studies
that investigated the merits of BoNT for LBP, but only one had a low risk of bias and evaluated patients with non‑specific LBP (N = 31).”
Putting it all together, the meta‑analysis concluded, “There is low quality evidence that BoNT injections improved pain, function, or both better than
saline injections and very low quality evidence that they were better than acupuncture or steroid injections. … Further research is very likely to have
an important impact on the estimate of effect and our confidence in it. Future trials should standardize patient populations, treatment protocols and
comparison groups, enlist more participants and include long‑term outcomes, cost‑benefit analysis and clinical relevance of findings.”
It takes a lot of careful work to establish that a medical treatment has a beneficial effect. Knowing how to analyze randomized controlled trials is a
crucial part of this work. Now that you know how to do that, you are well positioned to help medical and other professions establish cause‑and‑effect
relations.

12.3. Deflategate
On January 18, 2015, the Indianapolis Colts and the New England Patriots played the American Football Conference (AFC) championship game to
determine which of those teams would play in the Super Bowl. After the game, there were allegations that the Patriots’ footballs had not been inflated
as much as the regulations required; they were softer. This could be an advantage, as softer balls might be easier to catch.
For several weeks, the world of American football was consumed by accusations, denials, theories, and suspicions: the press labeled the topic
Deflategate, after the Watergate political scandal of the 1970’s. The National Football League (NFL) commissioned an independent analysis. In this
example, we will perform our own analysis of the data.
Pressure is often measured in pounds per square inch (psi). NFL rules stipulate that game balls must be inflated to have pressures in the range 12.5
psi and 13.5 psi. Each team plays with 12 balls. Teams have the responsibility of maintaining the pressure in their own footballs, but game officials
inspect the balls. Before the start of the AFC game, all the Patriots’ balls were at about 12.5 psi. Most of the Colts’ balls were at about 13.0 psi.
However, these pre‑game data were not recorded.
During the second quarter, the Colts intercepted a Patriots ball. On the sidelines, they measured the pressure of the ball and determined that it was
below the 12.5 psi threshold. Promptly, they informed officials.
At half‑time, all the game balls were collected for inspection. Two officials, Clete Blakeman and Dyrol Prioleau, measured the pressure in each of the
balls.
Here are the data. Each row corresponds to one football. Pressure is measured in psi. The Patriots ball that had been intercepted by the Colts was not
inspected at half‑time. Nor were most of the Colts’ balls – the officials simply ran out of time and had to relinquish the balls for the start of second
half play.
football = Table.read_table(path_data + 'deflategate.csv')
football.show()
Team Blakeman Prioleau
Patriots 11.5 11.8
Patriots 10.85 11.2
Patriots 11.15 11.5
Patriots 10.7 11
Patriots 11.1 11.45
Patriots 11.6 11.95
Patriots 11.85 12.3
Patriots 11.1 11.55
Patriots 10.95 11.35
Patriots 10.5 10.9
Patriots 10.9 11.35
Colts 12.7 12.35
Colts 12.75 12.3
Colts 12.5 12.95
Colts 12.55 12.15
For each of the 15 balls that were inspected, the two officials got different results. It is not uncommon that repeated measurements on the same
object yield different results, especially when the measurements are performed by different people. So we will assign to each the ball the average of
the two measurements made on that ball.
football = football.with_column(
'Combined', (football.column(1)+football.column(2))/2
).drop(1, 2)
football.show()

Team Combined
Patriots 11.65
Patriots 11.025
Patriots 11.325
Patriots 10.85
Patriots 11.275
Patriots 11.775
Patriots 12.075
Patriots 11.325
Patriots 11.15
Patriots 10.7
Patriots 11.125
Colts 12.525
Colts 12.525
Colts 12.725
Colts 12.35
At a glance, it seems apparent that the Patriots’ footballs were at a lower pressure than the Colts’ balls. Because some deflation is normal during the
course of a game, the independent analysts decided to calculate the drop in pressure from the start of the game. Recall that the Patriots’ balls had all
started out at about 12.5 psi, and the Colts’ balls at about 13.0 psi. Therefore the drop in pressure for the Patriots’ balls was computed as 12.5 minus
the pressure at half‑time, and the drop in pressure for the Colts’ balls was 13.0 minus the pressure at half‑time.
We can calculate the drop in pressure for each football, by first setting up an array of the starting values. For this we will need an array consisting of
11 values each of which is 12.5, and another consisting of four values each of which is all 13. We will use the NumPy function np.ones, which takes a
count as its argument and returns an array of that many elements, each of which is 1.
np.ones(11)

array([1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.])

patriots_start = 12.5 * np.ones(11)

colts_start = 13 * np.ones(4)
start = np.append(patriots_start, colts_start)
start

array([12.5, 12.5, 12.5, 12.5, 12.5, 12.5, 12.5, 12.5, 12.5, 12.5, 12.5,
13. , 13. , 13. , 13. ])

The drop in pressure for each football is the difference between the starting pressure and the combined pressure measurement.
drop = start - football.column('Combined')
football = football.with_column('Pressure Drop', drop)
football.show()

Team Combined Pressure Drop

Patriots 11.65 0.85
Patriots 11.025 1.475
Patriots 11.325 1.175
Patriots 10.85 1.65
Patriots 11.275 1.225
Patriots 11.775 0.725
Patriots 12.075 0.425
Patriots 11.325 1.175
Patriots 11.15 1.35
Patriots 10.7 1.8
Patriots 11.125 1.375
Colts 12.525 0.475
Colts 12.525 0.475
Colts 12.725 0.275
Colts 12.35 0.65
It looks as though the Patriots’ drops were larger than the Colts’. Let’s look at the average drop in each of the two groups. We no longer need the
combined scores.
football = football.drop('Combined')
football.group('Team', np.average)

Team Pressure Drop average

Colts 0.46875
Patriots 1.20227
The average drop for the Patriots was about 1.2 psi compared to about 0.47 psi for the Colts.
The question now is why the Patriots’ footballs had a larger drop in pressure, on average, than the Colts footballs. Could it be due to chance?

12.3.1. The Hypotheses

How does chance come in here? Nothing was being selected at random. But we can make a chance model by hypothesizing that the 11 Patriots’
drops look like a random sample of 11 out of all the 15 drops, with the Colts’ drops being the remaining four. That’s a completely specified chance
model under which we can simulate data. So it’s the null hypothesis.
For the alternative, we can take the position that the Patriots’ drops are too large, on average, to resemble a random sample drawn from all the drops.

12.3.2. Test Statistic

A natural statistic is the difference between the two average drops, which we will compute as “average drop for Patriots ‑ average drop for Colts”.
Large values of this statistic will favor the alternative hypothesis.
observed_means = football.group('Team', np.average).column(1)

observed_difference = observed_means.item(1) - observed_means.item(0)

observed_difference

0.733522727272728

This positive difference reflects the fact that the average drop in pressure of the Patriots’ footballs was greater than that of the Colts.
Just as we did in the previous section, we will write a function to calculate the difference between the mean drops in the two groups. The function
difference_of_means takes two arguments:

the name of the table of data

the label of the column containing the two group labels
It returns the difference between the mean drops of the two groups. We will calculate the difference as the Patriots’ drops minus the Colts’ drops as
before.
def difference_of_means(table, group_label):
reduced = table.select('Pressure Drop', group_label)
means_table = reduced.group(group_label, np.average)
means = means_table.column(1)
return means.item(1) - means.item(0)

difference_of_means(football, 'Team')

0.733522727272728

This is the same as the value we found earlier as the observed_difference.

12.3.3. Predicting the Statistic Under the Null Hypothesis

If the null hypothesis were true, then it shouldn’t matter which footballs are labeled Patriots and which are labeled Colts. The distributions of the two
sets of drops would be the same. We can simulate this by randomly shuffling the team labels.
shuffled_labels = football.sample(with_replacement=False).column(0)
original_and_shuffled = football.with_column('Shuffled Label', shuffled_labels)
original_and_shuffled.show()
Team Pressure Drop Shuffled Label
Patriots 0.85 Patriots
Patriots 1.475 Colts
Patriots 1.175 Colts
Patriots 1.65 Colts
Patriots 1.225 Patriots
Patriots 0.725 Patriots
Patriots 0.425 Patriots
Patriots 1.175 Patriots
Patriots 1.35 Patriots
Patriots 1.8 Patriots
Patriots 1.375 Colts
Colts 0.475 Patriots
Colts 0.475 Patriots
Colts 0.275 Patriots
Colts 0.65 Patriots
How do all the group averages compare?
difference_of_means(original_and_shuffled, 'Shuffled Label')

-0.5619318181818183

difference_of_means(original_and_shuffled, 'Team')

0.733522727272728

The two teams’ average drop values are closer when the team labels are randomly assigned to the footballs than they were for the two groups
actually used in the game.

12.3.4. Permutation Test

It’s time for a step that is now familiar. We will repeatedly simulate of the test statistic under the null hypothesis.
by repeatedly permuting the footballs and assigning random sets to the two teams.
As usual, we will start by writing a function one_simulated_difference that returns one simulated value of the difference between the mean pressure
drops of the groups labeled Patriots and Colts after randomly permuting the team labels of the footballs.
def one_simulated_difference():
shuffled_labels = football.sample(with_replacement = False
).column('Team')
shuffled_table = football.select('Pressure Drop').with_column(
'Shuffled Label', shuffled_labels)
return difference_of_means(shuffled_table, 'Shuffled Label')

We can now use a for loop and this function to create an array differences that contains 10,000 values of the test statistic simulated under the null
hypothesis.
differences = make_array()

repetitions = 10000
for i in np.arange(repetitions):
new_difference = one_simulated_difference()
differences = np.append(differences, new_difference)
12.3.5. Conclusion of the Test
To calculate the empirical P‑value, it’s important to recall the alternative hypothesis, which is that the Patriots’ drops are too large to be the result of
chance variation alone.
Larger drops for the Patriots favor the alternative hypothesis. So the p‑value is the chance (computed under the null hypothesis) of getting a test
statistic equal to our observed value of 0.733522727272728 or larger.
The figure below visualizes this calculation. It consists of the empirical distribution of the test statistic under the null hypothesis, with the observed
statistic marked in red on the horizontal axis and the area corresponding to the p‑value shaded in gold.
Table().with_column(
'Difference Between Group Averages', differences).hist(
left_end = observed_difference
)
plots.ylim(-0.1, 1.4)
plots.scatter(observed_difference, 0, color='red', s=30, zorder=3)
plots.title('Prediction Under the Null Hypothesis')
print('Observed Difference:', observed_difference)

Observed Difference: 0.733522727272728

By eye, the p‑value looks pretty small. We can confirm this by a calculation.
empirical_p = np.count_nonzero(differences >= observed_difference) / 10000
empirical_p

0.0026

As in previous examples of this test, the bulk of the distribution is centered around 0. Under the null hypothesis, the Patriots’ drops are a random
sample of all 15 drops, and therefore so are the Colts’. Therefore the two sets of drops should be about equal on average, and therefore their
difference should be around 0.
But the observed value of the test statistic is quite far away from the heart of the distribution. By any reasonable cutoff for what is “small”, the
empirical P‑value is small. So we end up rejecting the null hypothesis of randomness, and conclude that the Patriots drops were too large to reflect
chance variation alone.
The independent investigative team analyzed the data in several different ways, taking into account the laws of physics. The final report said,
“[T]he average pressure drop of the Patriots game balls exceeded the average pressure drop of the Colts balls by 0.45 to 1.02 psi,
depending on various possible assumptions regarding the gauges used, and assuming an initial pressure of 12.5 psi for the Patriots balls
and 13.0 for the Colts balls.”
– Investigative report commissioned by the NFL regarding the AFC Championship game on January 18, 2015
Our analysis shows an average pressure drop of about 0.73 psi, which is close to the center of the interval “0.45 to 1.02 psi” and therefore consistent
with the official analysis.
Remember that our test of hypotheses does not establish the reason why the difference is not due to chance. Establishing causality is usually more
complex than running a test of hypotheses.
But the all‑important question in the football world was about causation: the question was whether the excess drop of pressure in the Patriots’
footballs was deliberate. If you are curious about the answer given by the investigators, here is the full report.

13. Estimation
In the previous chapter we began to develop ways of inferential thinking. In particular, we learned how to use data to decide between two hypotheses
about the world. But often we just want to know how big something is.
For example, in an earlier chapter we investigated how many warplanes the enemy might have. In an election year, we might want to know what
percent of voters favor a particular candidate. To assess the current economy, we might be interested in the median annual income of households in
the United States.
In this chapter, we will develop a way to estimate an unknown parameter. Remember that a parameter is a numerical value associated with a
population.
To figure out the value of a parameter, we need data. If we have the relevant data for the entire population, we can simply calculate the parameter.
But if the population is very large – for example, if it consists of all the households in the United States – then it might be too expensive and time‑
consuming to gather data from the entire population. In such situations, data scientists rely on sampling at random from the population.
This leads to a question of inference: How to make justifiable conclusions about the unknown parameter, based on the data in the random sample?
We will answer this question by using inferential thinking.
A statistic based on a random sample can be a reasonable estimate of an unknown parameter in the population. For example, you might want to use
the median annual income of sampled households as an estimate of the median annual income of all households in the U.S.
But the value of any statistic depends on the sample, and the sample is based on random draws. So every time data scientists come up with an
estimate based on a random sample, they are faced with a question:
“How different could this estimate have been, if the sample had come out differently?”
In this chapter you will learn one way of answering this question. The answer will give you the tools to estimate a numerical parameter and quantify
the amount of error in your estimate.
We will start with a preliminary about percentiles. The most famous percentile is the median, often used in summaries of income data. Other
percentiles will be important in the method of estimation that we are about to develop. So we will start by defining percentiles carefully.

13.1. Percentiles
Numerical data can be sorted in increasing or decreasing order. Thus the values of a numerical data set have a rank order. A percentile is the value at
a particular rank.
For example, if your score on a test is on the 95th percentile, a common interpretation is that only 5% of the scores were higher than yours. The
median is the 50th percentile; it is commonly assumed that 50% the values in a data set are above the median.
But some care is required in giving percentiles a precise definition that works for all ranks and all lists. To see why, consider an extreme example
where all the students in a class score 75 on a test. Then 75 is a natural candidate for the median, but it’s not true that 50% of the scores are above
75. Also, 75 is an equally natural candidate for the 95th percentile or the 25th or any other percentile. Ties – that is, equal data values – have to be
taken into account when defining percentiles.
You also have to be careful about exactly how far up the list to go when the relevant index isn’t clear. For example, what should be the 87th percentile
of a collection of 10 values? The 8th value of the sorted collection, or the 9th, or somewhere in between?
In this section, we will give a definition that works consistently for all ranks and all lists.

13.1.1. A Numerical Example

Before giving a general definition of all percentiles, we will define the 80th percentile of a collection of values to be the smallest value in the collection
that is at least as large as 80% of all of the values.
For example, let’s consider the sizes of the five largest continents – Africa, Antarctica, Asia, North America, and South America – rounded to the
nearest million square miles.
sizes = make_array(12, 17, 6, 9, 7)

The 80th percentile is the smallest value that is at least as large as 80% of the elements of sizes, that is, four‑fifths of the five elements. That’s 12:
np.sort(sizes)

array([ 6, 7, 9, 12, 17])

The 80th percentile is a value on the list, namely 12. You can see that 80% of the values are less than or equal to it, and that it is the smallest value on
the list for which this is true.
Analogously, the 70th percentile is the smallest value in the collection that is at least as large as 70% of the elements of sizes. Now 70% of 5
elements is “3.5 elements”, so the 70th percentile is the 4th element on the list. That’s 12, the same as the 80th percentile for these data.

13.1.2. The percentile function

The percentile function takes two arguments: a rank between 0 and 100, and a array. It returns the corresponding percentile of the array.
percentile(70, sizes)

13.1.2.1. The General Definition

Let $p$ be a number between 0 and 100. The $p$th percentile of a collection is the smallest value in the collection that is at least as large as p% of
all the values.
By this definition, any percentile between 0 and 100 can be computed for any collection of values, and it is always an element of the collection.
In practical terms, suppose there are $n$ elements in the collection. To find the $p$th percentile:
Sort the collection in increasing order.
Find p% of n: $(p/100) \times n$. Call that $k$.
If $k$ is an integer, take the $k$th element of the sorted collection.
If $k$ is not an integer, round it up to the next integer, and take that element of the sorted collection.

13.1.2.2. Example
The table scores_and_sections contains one row for each student in a class of 359 students. The columns are the student’s discussion section and
midterm score.
scores_and_sections = Table.read_table(path_data + 'scores_by_section.csv')
scores_and_sections
Section Midterm
1 22
2 12
2 23
2 14
1 20
3 25
4 19
1 24
5 8
6 14
... (349 rows omitted)
scores_and_sections.select('Midterm').hist(bins=np.arange(-0.5, 25.6, 1))

What was the 85th percentile of the scores? To use the percentile function, create an array scores containing the midterm scores, and find the
85th percentile:
scores = scores_and_sections.column(1)

percentile(85, scores)

According to the percentile function, the 85th percentile was 22. To check that this is consistent with our new definition, let’s apply the definition
directly.
First, put the scores in increasing order:
sorted_scores = np.sort(scores_and_sections.column(1))

There are 359 scores in the array. So next, find 85% of 359, which is 305.15.
0.85 * 359

305.15

That’s not an integer. By our definition, the 85th percentile is the 306th element of sorted_scores, which, by Python’s indexing convention, is item
305 of the array.
# The 306th element of the sorted array

sorted_scores.item(305)
22

That’s the same as the answer we got by using percentile. In future, we will just use percentile.

13.1.3. Quartiles
The first quartile of a numercial collection is the 25th percentile. The terminology arises from the first quarter. The second quartile is the median, and
the third quartile is the 75th percentile.
For our scores data, those values are:
percentile(25, scores)

percentile(50, scores)

percentile(75, scores)

Distributions of scores are sometimes summarized by the “middle 50%” interval, between the first and third quartiles.

13.2. The Bootstrap

A data scientist is using the data in a random sample to estimate an unknown parameter. She uses the sample to calculate the value of a statistic that
she will use as her estimate.
Once she has calculated the observed value of her statistic, she could just present it as her estimate and go on her merry way. But she’s a data
scientist. She knows that her random sample is just one of numerous possible random samples, and thus her estimate is just one of numerous
plausible estimates.
By how much could those estimates vary? To answer this, it appears as though she needs to draw another sample from the population, and compute
a new estimate based on the new sample. But she doesn’t have the resources to go back to the population and draw another sample.
It looks as though the data scientist is stuck.
Fortunately, a brilliant idea called the bootstrap can help her out. Since it is not feasible to generate new samples from the population, the bootstrap
generates new random samples by a method called resampling: the new samples are drawn at random from the original sample.
In this section, we will see how and why the bootstrap works. In the rest of the chapter, we will use the bootstrap for inference.

13.2.1. Employee Compensation in the City of San Francisco

SF OpenData is a website where the City and County of San Francisco make some of their data publicly available. One of the data sets contains
compensation data for employees of the City. These include medical professionals at City‑run hospitals, police officers, fire fighters, transportation
workers, elected officials, and all other employees of the City.
Compensation data for the calendar year 2019 are in the table sf2019.
sf2019 = Table.read_table(path_data + 'san_francisco_2019.csv')

sf2019.show(3)
Organization Department Job Job Salary Overtime Benefits Compen
Group Family
Public Adult Information Trainer‑IS 91332 0 40059
Protection Probation Systems Journey
Public Adult Information Engineer‑IS 123241 0 49279 1
Protection Probation Systems Assistant
IS
Public Adult Information Business 115715 0 46752 1
Protection Probation Systems Analyst‑
Senior
... (44522 rows omitted)
There is one row for each of over 44,500 employees. There are numerous columns containing information about City departmental affiliation and
details of the different parts of the employee’s compensation package. Here is the row corresponding to London Breed, the Mayor of San Francisco in
2019.
sf2019.where('Job', 'Mayor')

Organization Department Job Family Job Salary Overtime Benefits

Group Compen
General Administrative
Administration Mayor & Mgmt Mayor 342974 0 98012 4
& Finance (Unrep)
We are going to study the final column, Total Compensation. That’s the employee’s salary plus the City’s contribution towards their retirement and
benefit plans.
Financial packages in a calendar year can sometimes be hard to understand as they depend on the date of hire, whether the employee is changing
jobs within the City, and so on. For example, the lowest values in the Total Compensation column look a little strange.
sf2019.sort('Total Compensation')
Organization Department Job Family Job Salary Overtime Bene
Group
Public Adult Probation & Deputy Probation 0 0
Protection Probation Parole Officer
Public Clerical,
Fire Secretarial
Protection Department & Senior Clerk Typist 0 0
Steno
Public Juvenile Correction & Counselor, Juvenile 0 0
Protection Court Detention Hall PERS
Public Clerical,
Protection Police Secretarial & Clerk Typist 0 0
Steno
Public Sheriff Correction & Deputy Sheriff 0 0
Protection Detention
Public Works, Sub‑
Airport Professional StdntDsgn
Transportation Commission 0 0
& Commerce Engineering Train2/Arch/Eng/Plng
Public Works, Clerical, Executive Secretary
Airport Secretarial
Transportation Commission & 1 0 0
& Commerce Steno
Public Works, Airport Payroll, Billing Senior Account
Transportation Commission & Accounting Clerk 0 0
& Commerce
Public Works, Airport Housekeeping
Transportation Commission & Laundry Custodian 0 0
& Commerce
Public Works, Airport Housekeeping
Transportation Commission & Laundry Custodian 0 0
& Commerce
... (44515 rows omitted)
For clarity of interpretation, we will focus our attention on those who had roughly the equivalent of a half‑time job or more for the whole year. At a
minimum wage of about 15 dollars per hour, and 20 hours per week for 52 weeks, that’s a salary of over 15,000 dollars.
sf2019 = sf2019.where('Salary', are.above(15000))

sf2019.num_rows

37103

13.2.2. Population and Parameter

Let this table of just over 37,000 rows be our population. Here is a histogram of the total compensations for the employees in this table.
sf_bins = np.arange(0, 726000, 25000)
sf2019.select('Total Compensation').hist(bins=sf_bins)
While most of the values are below 300,000 dollars, a few are quite a bit higher. For example, the total compensation of the Chief Investment Officer
was over 700,000 dollars. That is why the horizontal axis stretches quite far to the right of the visible bars.
sf2019.sort('Total Compensation', descending=True).show(2)

Organization Department Job Family Job Salary Overtime Benefits Co

Group
General Administrative Chief
Administration Retirement & Mgmt Investment 577633 0 146398
& Finance Services (Unrep) Officer
General
Administration Retirement
Services Unassigned Managing
Director 483072 0 134879
& Finance
... (37101 rows omitted)
Suppose the parameter in which we are interested is the median of the total compensations.
Since we have the luxury of having all of the data from the population, we can simply calculate the parameter:
pop_median = percentile(50, sf2019.column('Total Compensation'))
pop_median

135747.0

The median total compensation of all the employees was 135,747 dollars.
From a practical perspective, there is no reason for us to draw a sample to estimate this parameter since we simply know its value. But in this section
we are going to pretend we don’t know the value, and see how well we can estimate it based on a random sample.
In later sections, we will come down to earth and work in situations where the parameter is unknown. For now, we are all‑knowing.

13.2.3. A Random Sample and an Estimate

Let us draw a sample of 500 employees at random without replacement, and let the median total compensation of the sampled employees serve as
our estimate of the parameter.
our_sample = sf2019.sample(500, with_replacement=False)
our_sample.select('Total Compensation').hist(bins=sf_bins)

est_median = percentile(50, our_sample.column('Total Compensation'))

est_median

136835.0

The sample size is large. By the law of averages, the distribution of the sample resembles that of the population. Consequently the sample median is
quite comparable to the population median, though of course it is not exactly the same.
So now we have one estimate of the parameter. But had the sample come out differently, the estimate would have had a different value. We would like
to be able to quantify the amount by which the estimate could vary across samples. That measure of variability will help us measure how accurately
we can estimate the parameter.
To see how different the estimate would be if the sample had come out differently, we could just draw another sample from the population. But that
would be cheating. We are trying to mimic real life, in which we won’t have all the population data at hand.
Somehow, we have to get another random sample without sampling again from the population.

13.2.4. The Bootstrap: Resampling from the Sample

What we do have is a large random sample from the population. As we know, a large random sample is likely to resemble the population from which it
is drawn. This observation allows data scientists to lift themselves up by their own bootstraps: the sampling procedure can be replicated by sampling
from the sample.
Here are the steps of the bootstrap method for generating another random sample that resembles the population:
Treat the original sample as if it were the population.
Draw from the sample, at random with replacement, the same number of times as the original sample size.
It is important to resample the same number of times as the original sample size. The reason is that the variability of an estimate depends on the size
of the sample. Since our original sample consisted of 500 employees, our sample median was based on 500 values. To see how different the sample
could have been, we have to compare it to the median of other samples of size 500.
If we drew 500 times at random without replacement from our sample of size 500, we would just get the same sample back. By drawing with
replacement, we create the possibility for the new samples to be different from the original, because some employees might be drawn more than
once and others not at all.

13.2.5. Why the Bootstrap Works

Why is this a good idea? By the law of averages, the distribution of the original sample is likely to resemble the population, and the distributions of all
the “resamples” are likely to resemble the original sample. So the distributions of all the resamples are likely to resemble the population as well.

13.2.6. A Resampled Median

Recall that the sample method draws rows from a table with replacement by default, and when it is used without specifying a sample size, by default
the sample size equals the number of rows of the table. That’s perfect for the bootstrap! Here is one new sample drawn from the original sample, and
the corresponding sample median.
resample_1 = our_sample.sample()

resample_1.select('Total Compensation').hist(bins=sf_bins)
resampled_median_1 = percentile(50, resample_1.column('Total Compensation'))
resampled_median_1

141793.0

This value is an estimate of the population median.

By resampling again and again, we can get many such estimates, and hence an empirical distribution of the estimates.
resample_2 = our_sample.sample()
resampled_median_2 = percentile(50, resample_2.column('Total Compensation'))
resampled_median_2

135880.0

Let us collect this code and define a function one_bootstrap_median that returns one bootstrapped median of total compensation, based on
bootstrapping the original random sample that we called our_sample.
def one_bootstrap_median():
resampled_table = our_sample.sample()
bootstrapped_median = percentile(50, resampled_table.column('Total Compensation'))
return bootstrapped_median

Run the cell below a few times to see how the bootstrapped medians vary. Remember that each of them is an estimate of the population median.
one_bootstrap_median()

132175.0

13.2.7. Bootstrap Empirical Distribution of the Sample Median

We can now repeat the bootstrap process multiple times by running a for loop as usual. In each iteration, we will call the function
one_bootstrap_median to generate one value of the bootstrapped median based on our original sample our_sample. Then we will append the
boostrapped median to the collection array bstrap_medians.
Since we are asking for 5000 repetitions, the code might take a while to run. It has a lot of resampling to do!
num_repetitions = 5000
bstrap_medians = make_array()
for i in np.arange(num_repetitions):
bstrap_medians = np.append (bstrap_medians, one_bootstrap_median())

Here is an empirical histogram of the 5000 bootstrapped medians. The green dot is the population parameter: it is the median of the entire
population, which is what we are trying to estimate. In this example we happen to know its value, but we did not use it in the bootstrap process.
resampled_medians = Table().with_column('Bootstrap Sample Median', bstrap_medians)
median_bins=np.arange(120000, 160000, 2000)
resampled_medians.hist(bins = median_bins)

# Plotting parameters; you can ignore this code

parameter_green = '#32CD32'
plots.ylim(-0.000005, 0.00014)
plots.scatter(pop_median, 0, color=parameter_green, s=40, zorder=2);

It is important to remember that the green dot is fixed: it is 135,747 dollars, the population median. The empirical histogram is the result of random
draws, and will be situated randomly relative to the green dot.
Remember also that the point of all these computations is to estimate the population median, which is the green dot. Our estimates are all the
randomly generated sampled medians whose histogram you see above. We want the set of these estimates to contain the parameter. If it doesn’t,
then the estimates are off.

13.2.8. Do the Estimates Capture the Parameter?

How often does the empirical histogram of the resampled medians sit firmly over the green dot, and not just brush the dot with its tails or not cover it
at all? To answer this, we must define “sit firmly”. Let’s take that to mean “the middle 95% of the resampled medians contains the green dot”.
Here are the two ends of the “middle 95%” interval of resampled medians:
left = percentile(2.5, bstrap_medians)
left

129524.0

right = percentile(97.5, bstrap_medians)

right

143446.0

The population median of 135,747 dollars is between these two numbers. The interval and the population median are shown on the histogram below.
resampled_medians.hist(bins = median_bins)

# Plotting parameters; you can ignore this code

plots.ylim(-0.000005, 0.00014)
plots.plot([left, right], [0, 0], color='yellow', lw=3, zorder=1)
plots.scatter(pop_median, 0, color=parameter_green, s=40, zorder=2);
The “middle 95%” interval of estimates captured the parameter in our example. But was that a fluke?
To see how frequently the interval contains the parameter, we have to run the entire process over and over again. Specifically, we will replicate the
following process 100 times:
Draw an original random sample of size 500 from the population.
Carry out 5000 replications of the bootstrap process and generate the “middle 95%” interval of resampled medians.
We will end up with 100 intervals, and count how many of them contain the population median.
Spoiler alert: The statistical theory of the bootstrap says that the number should be around 95. It may be in the low 90s or high 90s, but we don’t
expect it to be much farther off 95 than that.
We will start by writing a function bootstrap_median that takes two arguments: the name of the table containing the original random sample, and the
number of bootstrap samples to draw. It returns an array of bootstrapped medians, one from each boostrap sample.
def bootstrap_median(original_sample, num_repetitions):
medians = make_array()
for i in np.arange(num_repetitions):
new_bstrap_sample = original_sample.sample()
new_bstrap_median = percentile(50, new_bstrap_sample.column('Total
Compensation'))
medians = np.append(medians, new_bstrap_median)
return medians

Now we will write a for loop that calls this function 100 times and collects the “middle 95%” of the bootstrapped medians each time.
The cell below will take several minutes to run since it has to perform 100 replications of sampling 500 times at random from the table and generating
5000 bootstrapped samples.
# THE BIG SIMULATION: This one takes several minutes.

# Generate 100 intervals and put the endpoints in the table intervals

left_ends = make_array()
right_ends = make_array()

for i in np.arange(100):
original_sample = sf2019.sample(500, with_replacement=False)
medians = bootstrap_median(original_sample, 5000)
left_ends = np.append(left_ends, percentile(2.5, medians))
right_ends = np.append(right_ends, percentile(97.5, medians))

intervals = Table().with_columns(
'Left', left_ends,
'Right', right_ends
)

For each of the 100 replications of the entire process, we get one interval of estimates of the median.
intervals
Left Right
125093 139379
129925 140757
133955 146369
129335 140847
132756 145429
130167 143200
125935 138491
131092 142472
128509 140462
131270 145998
... (90 rows omitted)
The good intervals are those that contain the parameter we are trying to estimate. Typically the parameter is unknown, but in this section we happen
to know what the parameter is.
pop_median

135747.0

How many of the 100 intervals contain the population median? That’s the number of intervals where the left end is below the population median and
the right end is above.
intervals.where(
'Left', are.below(pop_median)).where(
'Right', are.above(pop_median)).num_rows

It takes many minutes to construct all the intervals, but try it again if you have the patience. Most likely, about 95 of the 100 intervals will be good
ones: they will contain the parameter.
It’s hard to show you all the intervals on the horizontal axis as they have large overlaps – after all, they are all trying to estimate the same parameter.
The graphic below shows each interval on the same axes by stacking them vertically. The vertical axis is simply the number of the replication from
which the interval was generated.
The green line is where the parameter is. It has a fixed position since the parameter is fixed.
Good intervals cover the parameter. There are approximately 95 of these, typically.
If an interval doesn’t cover the parameter, it’s a dud. The duds are the ones where you can see “daylight” around the green line. There are very few of
them – about 5 out of 100, typically – but they do happen.
Any method based on sampling has the possibility of being off. The beauty of methods based on random sampling is that we can quantify how often
they are likely to be off.
To summarize what the simulation shows, suppose you are estimating the population median by the following process:
Draw a large random sample from the population.
Bootstrap your random sample and get an estimate from the new random sample.
Repeat the above bootstrap step thousands of times, and get thousands of estimates.
Pick off the “middle 95%” interval of all the estimates.
That gives you one interval of estimates. If 99 other people repeat the entire process, starting with a new random sample each time, then you will
end up with 100 such intervals. About 95 of these 100 intervals will contain the population parameter.
In other words, this process of estimation captures the parameter about 95% of the time.
You can replace 95% by a different value, as long as it’s not 100. Suppose you replace 95% by 80% and keep the sample size fixed at 500. Then your
intervals of estimates will be shorter than those we simulated here, because the “middle 80%” is a smaller range than the “middle 95%”. If you keep
repeating this process, only about 80% of your intervals will contain the parameter.

13.3. Confidence Intervals

We have developed a method for estimating a parameter by using random sampling and the bootstrap. Our method produces an interval of
estimates, to account for chance variability in the random sample. By providing an interval of estimates instead of just one estimate, we give
ourselves some wiggle room.
In the previous example we saw that our process of estimation produced a good interval about 95% of the time, a “good” interval being one that
contains the parameter. We say that we are 95% confident that the process results in a good interval. Our interval of estimates is called a 95%
confidence interval for the parameter, and 95% is called the confidence level of the interval.
The method is called the boostrap percentile method because the interval is formed by picking off two percentiles of the bootstrapped estimates.
The situation in the previous example was a bit unusual. Because we happened to know the value of the parameter, we were able to check whether an
interval was good or a dud, and this in turn helped us to see that our process of estimation captured the parameter about 95 out of every 100 times
we used it.
But usually, data scientists don’t know the value of the parameter. That is the reason they want to estimate it in the first place. In such situations, they
provide an interval of estimates for the unknown parameter by using methods like the one we have developed. Because of statistical theory and
demonstrations like the one we have seen, data scientists can be confident that their process of generating the interval results in a good interval a
known percent of the time.
13.3.1. Estimating a Population Median
We will now use the bootstrap method to estimate an unknown population median. You have encountered the dataset before. It comes from a sample
of newborns in a large hospital system. we will treat it as if it were a simple random sample though the sampling was done in multiple stages. Stat
Labs by Deborah Nolan and Terry Speed has details about a larger dataset from which this set is drawn.
The table births contains the following variables for mother‑baby pairs: the baby’s birth weight in ounces, the number of gestational days (the
number of days the mother was pregnant), the mother’s age in completed years, the mother’s height in inches, pregnancy weight in pounds, and
whether or not the mother smoked during pregnancy.
births = Table.read_table(path_data + 'baby.csv')

births.show(3)

Birth Gestational Maternal Maternal Maternal Pregnancy Maternal

Weight Days Age Height Weight Smoker
120 284 27 62 100 False
113 282 33 64 135 False
128 279 28 64 115 True
... (1171 rows omitted)
Birth weight is an important factor in the health of a newborn infant. Smaller babies tend to need more medical care in their first days than larger
newborns. It is therefore helpful to have an estimate of birth weight before the baby is born. One way to do this is to examine the relationship
between birth weight and the number of gestational days.
A simple measure of this relationship is the ratio of birth weight to the number of gestational days. The table ratios contains the first two columns of
baby, as well as a column of the ratios. The first entry in that column was calculated as follows:
\[ \frac{120~\mbox{ounces}}{284~\mbox{days}} ~\approx ~ 0.4225~ \mbox{ounces per day} \]
ratios = births.select('Birth Weight', 'Gestational Days').with_columns(
'Ratio BW:GD', births.column('Birth Weight')/births.column('Gestational Days')
)

ratios

Birth Weight Gestational Days Ratio BW GD

120 284 0.422535
113 282 0.400709
128 279 0.458781
108 282 0.382979
136 286 0.475524
138 244 0.565574
132 245 0.538776
120 289 0.415225
143 299 0.478261
140 351 0.39886
... (1164 rows omitted)
Here is a histogram of the ratios.
ratios.select('Ratio BW:GD').hist()
At first glance the histogram looks quite symmetric, with the density at its maximum over the interval 0.4 ounces per day to 0.45 ounces per day. But
a closer look reveals that some of the ratios were quite large by comparison. The maximum value of the ratios was just over 0.78 ounces per day,
almost double the typical value.
ratios.sort('Ratio BW:GD', descending=True).take(0)

Birth Weight Gestational Days Ratio BW GD

116 148 0.783784
The median gives a sense of the typical ratio because it is unaffected by the very large or very small ratios. The median ratio in the sample is about
0.429 ounces per day.
percentile(50, ratios.column(2))

0.42907801418439717

But what was the median in the population? We don’t know, so we will estimate it.
Our method will be exactly the same as in the previous section. We will bootstrap the sample 5,000 times resulting in 5,000 estimates of the median.
Our 95% confidence interval will be the “middle 95%” of all of our estimates.

13.3.1.1. Constructing a Bootstrap Confidence Interval

We will start by defining a function one_bootstrap_median. It will bootstrap the sample and return one the median ratio in the bootstrapped sample.
def one_bootstrap_median():
resample = ratios.sample()
return percentile(50, resample.column('Ratio BW:GD'))

Run the cell below to see how the bootstrapped ratios vary. Remember that each of them is an estimate of the unknown ratio in the population.
one_bootstrap_median()

0.43010752688172044

Now we can use a for loop to generate 5000 bootstrapped medians.

# Generate medians from 5000 bootstrap samples
num_repetitions = 5000
bstrap_medians = make_array()
for i in np.arange(num_repetitions):
bstrap_medians = np.append(bstrap_medians, one_bootstrap_median())

# Get the endpoints of the 95% confidence interval

left = percentile(2.5, bstrap_medians)
right = percentile(97.5, bstrap_medians)

make_array(left, right)
array([0.42545455, 0.43272727])

The 95% confidence interval goes from about 0.425 ounces per day to about 0.433 ounces per day. We are estimating the median “birth weight to
gestational days” ratio in the population is somewhere in the interval 0.425 ounces per day to 0.433 ounces per day.
The estimate of 0.429 based on the original sample happens to be half‑way in between the two ends of the interval, though that need not be true in
general.
To visualize our results, let us draw the empirical histogram of our bootstrapped medians and place the confidence interval on the horizontal axis.
resampled_medians = Table().with_columns(
'Bootstrap Sample Median', bstrap_medians
)
resampled_medians.hist(bins=15)
plots.plot([left, right], [0, 0], color='yellow', lw=8);

This histogram and interval resembles those we drew in the previous section, with one big difference – there is no green dot showing where the
parameter is. We don’t know where that dot should be, or whether it is even in the interval.
We just have an interval of estimates. It is a 95% confidence interval of estimates, because the process that generates it produces a good interval
about 95% of the time. That certainly beats guessing the ratio at random!
Keep in mind that this interval is an approximate 95% confidence interval. There are many approximations involved in its computation. The
approximation is not bad, but it is not exact.

13.3.2. Estimating a Population Average

What we have done for medians can be done for averages as well. Suppose we want to estimate the average age of the mothers in the population. A
natural estimate is the average age of the mothers in the sample. Here is the distribution of their ages, and their average age which was about 27.2
years.
births.select('Maternal Age').hist()

np.average(births.column('Maternal Age'))
27.228279386712096

What was the average age of the mothers in the population? We don’t know the value of this parameter.
Let’s estimate the unknown parameter by the bootstrap method. To do this, we will adapt the code for bootstrap_median to instead define the
function bootstrap_mean. The code is the same except that the statistics are means (that is, averages) instead of medians, and are collected in an
array called bstrap_means instead of bstrap_medians.
def one_bootstrap_mean():
resample = births.sample()
return np.average(resample.column('Maternal Age'))

# Generate means from 5000 bootstrap samples

num_repetitions = 5000
bstrap_means = make_array()
for i in np.arange(num_repetitions):
bstrap_means = np.append(bstrap_means, one_bootstrap_mean())

# Get the endpoints of the 95% confidence interval

left = percentile(2.5, bstrap_means)
right = percentile(97.5, bstrap_means)

make_array(left, right)

array([26.90630324, 27.55962521])

The 95% confidence interval goes from about 26.9 years to about 27.6 years. That is, we are estimating that the average age of the mothers in the
population is somewhere in the interval 26.9 years to 27.6 years.
Notice how close the two ends are to the average of about 27.2 years in the original sample. The sample size is very large – 1,174 mothers – and so
the sample averages don’t vary much. We will explore this observation further in the next chapter.
The empirical histogram of the 5,000 bootstrapped mean ages is shown below, along with the 95% confidence interval for the population mean age.
resampled_means = Table().with_columns(
'Bootstrap Sample Mean', bstrap_means
)
resampled_means.hist(bins=15)
plots.plot([left, right], [0, 0], color='yellow', lw=8);

Once again, the average of the original sample (27.23 years) is close to the center of the interval. That’s not very surprising, because each
bootstrapped sample is drawn from that same original sample. The averages of the bootstrapped samples are about symmetrically distributed on
either side of the average of the sample from which they were drawn.
Notice also that the empirical histogram of the resampled means has roughly a symmetric bell shape, even though the histogram of the sampled ages
was not symmetric at all:
births.select('Maternal Age').hist()
This is a consequence of the Central Limit Theorem of probability and statistics. In later sections, we will see what the theorem says.

13.3.3. An 80% Confidence Interval

You can use the bootstrapped sample means to construct an interval of any level of confidence. For example, to construct an 80% confidence
interval for the mean age in the population, you would take the “middle 80%” of the resampled means. So you would want 10% of the distribution in
each of the two tails, and hence the endpoints would be the 10th and 90th percentiles of the resampled means.
left_80 = percentile(10, bstrap_means)
right_80 = percentile(90, bstrap_means)
make_array(left_80, right_80)

array([27.01277683, 27.44293015])

resampled_means.hist(bins=15)
plots.plot([left_80, right_80], [0, 0], color='yellow', lw=8);

This 80% confidence interval is much shorter than the 95% confidence interval. It only goes from about 27.0 years to about 27.4 years. While that’s a
tight set of estimates, you know that this process only produces a good interval about 80% of the time.
The earlier process produced a wider interval but we had more confidence in the process that generated it.
To get a narrow confidence interval at a high level of confidence, you’ll have to start with a larger sample. We’ll see why in the next chapter.

13.3.4. Estimating a Population Proportion

In the sample, 39% of the mothers smoked during pregnancy.
births.where('Maternal Smoker', are.equal_to(True)).num_rows / births.num_rows

0.3909710391822828

Remember that a proportion is an average of zeros and ones. So the proportion of mothers who smoked could also be calculated using array
operations as follows.
smoking = births.column('Maternal Smoker')
np.count_nonzero(smoking) / len(smoking)

0.3909710391822828

What percent of mothers in the population smoked during pregnancy? This is an unknown parameter which we can estimate by a bootstrap
confidence interval. The steps are analogous to those we took to estimate the population median and mean.
In a process that is now familiar, will start by defining a function one_bootstrap_proportion that bootstraps the sample and returns the proportion of
smokers in the bootstrapped sample. Then we will call the function multiple times using a for loop, and get the 2.5th perentile and 97.5th percentiles
of the bootstrapped proportions.
def one_bootstrap_proportion():
resample = births.sample()
smoking = resample.column('Maternal Smoker')
return np.count_nonzero(smoking) / len(smoking)

# Generate proportions from 5000 bootstrap samples

bstrap_proportions = make_array()
num_repetitions = 5000
for i in np.arange(num_repetitions):
bstrap_proportions = np.append(bstrap_proportions, one_bootstrap_proportion())

# Get the endpoints of the 95% confidence interval

left = percentile(2.5, bstrap_proportions)
right = percentile(97.5, bstrap_proportions)

make_array(left, right)

array([0.36286201, 0.41908007])

The confidence interval goes from about 36% to about 42%.

resampled_proportions = Table().with_columns(
'Bootstrap Sample Proportion', bstrap_proportions
)
resampled_proportions.hist(bins=15)
plots.plot([left, right], [0, 0], color='yellow', lw=8);

13.3.5. Care in Using the Bootstrap Percentile Method

The bootstrap is an elegant and powerful method. Before using it, it is important to keep some points in mind.
Start with a large random sample. If you don’t, the method might not work. Its success is based on large random samples (and hence also
resamples from the sample) resembling the population. The Law of Averages says that this is likely to be true provided the random sample is
large.
To approximate the probability distribution of a statistic, it is a good idea to replicate the resampling procedure as many times as possible. A few
thousand replications will result in decent approximations to the distribution of sample median, especially if the distribution of the population
has one peak and is fairly symmetric. We used 5,000 replications in our examples but would recommend 10,000 in general.
The bootstrap percentile method works well for estimating the population median or mean based on a large random sample. However, it has
limitations, as do all methods of estimation. For example, it is not expected to do well in the following situations.
The goal is to estimate the minimum or maximum value in the population, or a very low or very high percentile, or parameters that are
greatly influenced by rare elements of the population.
The probability distribution of the statistic is not roughly bell shaped.
The original sample is very small, say less than 10 or 15.

13.4. Using Confidence Intervals

A confidence interval has a single purpose – to estimate an unknown parameter based on data in a random sample. In the last section, we said that
the interval (36%, 42%) was an approximate 95% confidence interval for the percent of smokers among mothers in the population. That was a formal
way of saying that by our estimate, the percent of smokers among the mothers in the population was somewhere between 36% and 42%, and that
our process of estimation is correct about 95% of the time.
It is important to resist the impulse to use confidence intervals for other purposes. For example, recall that we calculated the interval (26.9 years, 27.6
years) as an approximate 95% confidence interval for the average age of mothers in the population. A dismayingly common misuse of the interval is
to conclude that about 95% of the women were between 26.9 years and 27.6 years old. You don’t need to know much about confidence intervals to
see that this can’t be right – you wouldn’t expect 95% of mothers to all be within a few months of each other in age. Indeed, the histogram of the
sampled ages shows quite a bit of variation.
births = Table.read_table(path_data + 'baby.csv')

births.select('Maternal Age').hist()

A small percent of the sampled ages are in the (26.9, 27.6) interval, and you would expect a similar small percent in the population. The interval just
estimates one number: the average of all the ages in the population.
However, estimating a parameter by confidence intervals does have an important use besides just telling us roughly how big the parameter is.

13.4.1. Using a Confidence Interval to Test Hypotheses

Our approximate 95% confidence interval for the average age in the population goes from 26.9 years to 27.6 years. Suppose someone wants to test
the following hypotheses:
Null hypothesis: The average age in the population is 30 years.
Alternative hypothesis: The average age in the population is not 30 years.
Then, if you were using the 5% cutoff for the p‑value, you would reject the null hypothesis. This is because 30 is not in the 95% confidence interval
for the population average. At the 5% level of significance, 30 is not a plausible value for the population average.
This use of confidence intervals is the result of a duality between confidence intervals and tests: if you are testing whether or not the population
mean is a particular value x, and you use the 5% cutoff for the p‑value, then you will reject the null hypothesis if x is not in your 95% confidence
interval for the mean.
This can be established by statistical theory. In practice, it just boils down to checking whether or not the value specified in the null hypothesis lies in
the confidence interval.
If you were using the 1% cutoff for the P‑value, you would have to check if the value specified in the null hypothesis lies in a 99% confidence interval
for the population mean.
To a rough approximation, these statements are also true for population proportions, provided the sample is large.
While we now have a way of using confidence intervals to test a particular kind of hypothesis, you might wonder about the value of testing whether or
not the average age in a population is equal to 30. Indeed, the value isn’t clear. But there are some situations in which a test of this kind of hypothesis
is both natural and useful.

13.4.2. Comparing Baseline and Post‑Treatment Scores

We will study this in the context of data that are a subset of the information gathered in a randomized controlled trial about treatments for Hodgkin’s
disease. Hodgkin’s disease is a cancer that typically affects young people. The disease is curable but the treatment can be very harsh. The purpose
of the trial was to come up with dosage that would cure the cancer but minimize the adverse effects on the patients.
This table hodgkins contains data on the effect that the treatment had on the lungs of 22 patients. The columns are:
Height in cm
A measure of radiation to the mantle (neck, chest, under arms)
A measure of chemotherapy
A score of the health of the lungs at baseline, that is, at the start of the treatment; higher scores correspond to more healthy lungs
The same score of the health of the lungs, 15 months after treatment
hodgkins = Table.read_table(path_data + 'hodgkins.csv')

hodgkins.show(3)

height rad chemo base month15

164 679 180 160.57 87.77
168 311 180 98.24 67.62
173 388 239 129.04 133.33
... (19 rows omitted)
We will compare the baseline and 15‑month scores. As each row corresponds to one patient, we say that the sample of baseline scores and the
sample of 15‑month scores are paired ‑ they are not just two sets of 22 values each, but 22 pairs of values, one for each patient.
At a glance, you can see that the 15‑month scores tend to be lower than the baseline scores – the sampled patients’ lungs seem to be doing worse 15
months after the treatment. This is confirmed by the mostly positive values in the column drop, the amount by which the score dropped from baseline
to 15 months.
hodgkins = hodgkins.with_columns(
'drop', hodgkins.column('base') - hodgkins.column('month15')
)

hodgkins
height rad chemo base month15 drop
164 679 180 160.57 87.77 72.8
168 311 180 98.24 67.62 30.62
173 388 239 129.04 133.33 ‑4.29
157 370 168 85.41 81.28 4.13
160 468 151 67.94 79.26 ‑11.32
170 341 96 150.51 80.97 69.54
163 453 134 129.88 69.24 60.64
175 529 264 87.45 56.48 30.97
185 392 240 149.84 106.99 42.85
178 479 216 92.24 73.43 18.81
... (12 rows omitted)
hodgkins.select('drop').hist(bins=np.arange(-20, 81, 20))

np.average(hodgkins.column('drop'))

28.615909090909096

In the sample, the average drop is about 28.6. But could this be the result of chance variation? The data are from a random sample. Could it be that in
the entire population of patients, the average drop is just 0?
To answer this, we can set up two hypotheses:
Null hypothesis: In the population, the average drop is 0.
Alternative hypothesis: In the population, the average drop is not 0.
To test this hypothesis with a 1% cutoff for the p‑value, let’s construct an approximate 99% confidence interval for the average drop in the
population.
def one_bootstrap_mean():
resample = hodgkins.sample()
return np.average(resample.column('drop'))

# Generate 10,000 bootstrap means

num_repetitions = 10000
bstrap_means = make_array()
for i in np.arange(num_repetitions):
bstrap_means = np.append(bstrap_means, one_bootstrap_mean())

# Get the endpoints of the 99% confidence interval

left = percentile(0.5, bstrap_means)
right = percentile(99.5, bstrap_means)

make_array(left, right)
array([17.46863636, 40.97681818])

resampled_means = Table().with_columns(
'Bootstrap Sample Mean', bstrap_means
)
resampled_means.hist()
plots.plot([left, right], [0, 0], color='yellow', lw=8);

The 99% confidence interval for the average drop in the population goes from about 17 to about 40. The interval doesn’t contain 0. So we reject the
null hypothesis.
But notice that we have done better than simply concluding that the average drop in the population isn’t 0. We have estimated how big the average
drop is. That’s a more useful result than just saying, “It’s not 0.”
A note on accuracy: Our confidence interval is quite wide, for two main reasons:
The confidence level is high (99%).
The sample size is relatively small compared to those in our earlier examples.
In the next chapter, we will examine how the sample size affects accuracy. We will also examine how the empirical distributions of sample means so
often come out bell shaped even though the distributions of the underlying data are not bell shaped at all.

13.4.3. Endnote
The terminology of a field usually comes from the leading researchers in that field. Brad Efron, who first proposed the bootstrap technique, used a
term that has American origins. Not to be outdone, Chinese statisticians have proposed their own method.

14. Why the Mean Matters

In this course we have studied several different statistics, including total variation distance, the maximum, the median, and also the mean. Under
clear assumptions about randomness, we have drawn empirical distributions of all of these statistics. Some, like the maximum and the total variation
distance, have distributions that are clearly skewed in one direction or the other. But the empirical distribution of the sample mean has almost always
turned out close to bell‑shaped, regardless of the population being studied.
If a property of random samples is true regardless of the population, it becomes a powerful tool for inference because we rarely know much about the
data in the entire population. The distribution of the mean of a large random sample falls into this category of properties. That is why random sample
means are extensively used in data science.
In this chapter, we will study means and what we can say about them with only minimal assumptions about the underlying populations. Question that
we will address include:
What exactly does the mean measure?
How close to the mean are most of the data?
How is the sample size related to the variability of the sample mean?
Why do empirical distributions of random sample means come out bell shaped?
How can we use sample means effectively for inference?
14.1. Properties of the Mean
In this course, we have used the words “average” and “mean” interchangeably, and will continue to do so. The definition of the mean will be familiar to
you from your high school days or even earlier.
Definition. The average or mean of a collection of numbers is the sum of all the elements of the collection, divided by the number of elements in the
collection.
The methods np.average and np.mean return the mean of an array.
not_symmetric = make_array(2, 3, 3, 9)

np.average(not_symmetric)

4.25

np.mean(not_symmetric)

4.25

14.1.1. Basic Properties

The definition and the example above point to some properties of the mean.
It need not be an element of the collection.
It need not be an integer even if all the elements of the collection are integers.
It is somewhere between the smallest and largest values in the collection.
It need not be halfway between the two extremes; it is not in general true that half the elements in a collection are above the mean.
If the collection consists of values of a variable measured in specified units, then the mean has the same units too.
We will now study some other properties that are helpful in understanding the mean and its relation to other statistics.

14.1.2. The Mean is a “Smoother”

You can think of taking the mean as an “equalizing” or “smoothing” operation. For example, imagine the entries in not_symmetric above as the dollars
in the pockets of four different people. To get the mean, you first put all of the money into one big pot and then divide it evenly among the four
people. They had started out with different amounts of money in their pockets ($2, $3, $3, and $9), but now each person has $4.25, the mean
amount.

14.1.3. Proportions are Means

If a collection consists only of ones and zeroes, then the sum of the collection is the number of ones in it, and the mean of the collection is the
proportion of ones.
zero_one = make_array(1, 1, 1, 0)
sum(zero_one)

np.mean(zero_one)

0.75

You can replace 1 by the Boolean True and 0 by False:

np.mean(make_array(True, True, True, False))
0.75

Because proportions are a special case of means, results about random sample means apply to random sample proportions as well.

14.1.4. The Mean and the Histogram

The mean of the collection {2, 3, 3, 9} is 4.25, which is not the “halfway point” of the data. So then what does the mean measure?
To see this, notice that the mean can be calculated in different ways.
\[\begin{split}\begin{align*} \mbox{mean} ~ &=~ 4.25 \\ \\ &=~ \frac{2 + 3 + 3 + 9}{4} \\ \\ &=~ 2 \cdot \frac{1}{4} ~~ + ~~ 3 \cdot \frac{1}{4} ~~ + ~~ 3
\cdot \frac{1}{4} ~~ + ~~ 9 \cdot \frac{1}{4} \\ \\ &=~ 2 \cdot \frac{1}{4} ~~ + ~~ 3 \cdot \frac{2}{4} ~~ + ~~ 9 \cdot \frac{1}{4} \\ \\ &=~ 2 \cdot 0.25 ~~
+ ~~ 3 \cdot 0.5 ~~ + ~~ 9 \cdot 0.25 \end{align*}\end{split}\]
The last expression is an example of a general fact: when we calculate the mean, each distinct value in the collection is weighted by the proportion of
times it appears in the collection.
This has an important consequence. The mean of a collection depends only on the distinct values and their proportions, not on the number of
elements in the collection. In other words, the mean of a collection depends only on the distribution of values in the collection.
Therefore, if two collections have the same distribution, then they have the same mean.
For example, here is another collection that has the same distribution as not_symmetric and hence the same mean.
not_symmetric

array([2, 3, 3, 9])

same_distribution = make_array(2, 2, 3, 3, 3, 3, 9, 9)
np.mean(same_distribution)

4.25

The mean is a physical attribute of the histogram of the distribution. Here is the histogram of the distribution of not_symmetric or equivalently the
distribution of same_distribution.

Imagine the histogram as a figure made out of cardboard attached to a wire that runs along the horizontal axis, and imagine the bars as weights
attached at the values 2, 3, and 9. Suppose you try to balance this figure on a point on the wire. If the point is near 2, the figure will tip over to the
right. If the point is near 9, the figure will tip over to the left. Somewhere in between is the point where the figure will balance; that point is the 4.25,
the mean.
The mean is the center of gravity or balance point of the histogram.
To understand why that is, it helps to know some physics. The center of gravity is calculated exactly as we calculated the mean, by using the distinct
values weighted by their proportions.
Because the mean is a balance point, it is sometimes displayed as a fulcrum or triangle at the base of the histogram.
14.1.5. The Mean and the Median
If a student’s score on a test is below average, does that imply that the student is in the bottom half of the class on that test?
Happily for the student, the answer is, “Not necessarily.” The reason has to do with the relation between the average, which is the balance point of
the histogram, and the median, which is the “half‑way point” of the data.
The relationship is easy to see in a simple example. Here is a histogram of the collection {2, 3, 3, 4} which is in the array symmetric. The distribution is
symmetric about 3. The mean and the median are both equal to 3.
symmetric = make_array(2, 3, 3, 4)

np.mean(symmetric)

3.0

percentile(50, symmetric)

In general, for symmetric distributions, the mean and the median are equal.
What if the distribution is not symmetric? Let’s compare symmetric and not_symmetric.
The blue histogram represents the original symmetric distribution. The gold histogram of not_symmetric starts out the same as the blue at the left
end, but its rightmost bar has slid over to the value 9. The brown part is where the two histograms overlap.
The median and mean of the blue distribution are both equal to 3. The median of the gold distribution is also equal to 3, though the right half is
distributed differently from the left.
But the mean of the gold distribution is not 3: the gold histogram would not balance at 3. The balance point has shifted to the right, to 4.25.
In the gold distribution, 3 out of 4 entries (75%) are below average. The student with a below average score can therefore take heart. He or she might
be in the majority of the class.
In general, if the histogram has a tail on one side (the formal term is “skewed”), then the mean is pulled away from the median in the
direction of the tail.

14.1.5.1. Example
The table sf2015 contains salary and benefits data for San Francisco City employees in 2015. As before, we will restrict our analysis to those who had
the equivalent of at least half‑time employment for the year.
sf2015 = Table.read_table(path_data + 'san_francisco_2015.csv').where('Salaries',
are.above(10000))

As we saw earlier, the highest compensation was above $600,000 but the vast majority of employees had compensations below $300,000.
sf2015.select('Total Compensation').hist(bins = np.arange(10000, 700000, 25000))

This histogram is skewed to the right; it has a right‑hand tail.

The mean gets pulled away from the median in the direction of the tail. So we expect the mean compensation to be larger than the median, and that
is indeed the case.
compensation = sf2015.column('Total Compensation')
percentile(50, compensation)

110305.79
np.mean(compensation)

114725.98411824222

Distributions of incomes of large populations tend to be right skewed. When the bulk of a population has middle to low incomes, but a very small
proportion has very high incomes, the histogram has a long, thin tail to the right.
The mean income is affected by this tail: the farther the tail stretches to the right, the larger the mean becomes. But the median is not affected by
values at the extremes of the distribution. That is why economists often summarize income distributions by the median instead of the mean.

14.2. Variability
The mean tells us where a histogram balances. But in almost every histogram we have seen, the values spread out on both sides of the mean. How
far from the mean can they be? To answer this question, we will develop a measure of variability about the mean.
We will start by describing how to calculate the measure. Then we will see why it is a good measure to calculate.

14.2.1. The Rough Size of Deviations from Average

For simplicity, we will begin our calculations in the context of a simple array any_numbers consisting of just four values. As you will see, our method
will extend easily to any other array of values.
any_numbers = make_array(1, 2, 2, 10)

The goal is to measure roughly how far off the numbers are from their average. To do this, we first need the average:
# Step 1. The average.

mean = np.mean(any_numbers)
mean

3.75

Next, let’s find out how far each value is from the mean. These are called the deviations from the average. A “deviation from average” is just a value
minus the average. The table calculation_steps displays the results.
# Step 2. The deviations from average.

deviations = any_numbers - mean

calculation_steps = Table().with_columns(
'Value', any_numbers,
'Deviation from Average', deviations
)
calculation_steps

Value Deviation from Average

1 ‑2.75
2 ‑1.75
2 ‑1.75
10 6.25
Some of the deviations are negative; those correspond to values that are below average. Positive deviations correspond to above‑average values.
To calculate roughly how big the deviations are, it is natural to compute the mean of the deviations. But something interesting happens when all the
deviations are added together:
sum(deviations)

0.0
The positive deviations exactly cancel out the negative ones. This is true of all lists of numbers, no matter what the histogram of the list looks like: the
sum of the deviations from average is zero.
Since the sum of the deviations is 0, the mean of the deviations will be 0 as well:
np.mean(deviations)

0.0

Because of this, the mean of the deviations is not a useful measure of the size of the deviations. What we really want to know is roughly how big the
deviations are, regardless of whether they are positive or negative. So we need a way to eliminate the signs of the deviations.
There are two time‑honored ways of losing signs: the absolute value, and the square. It turns out that taking the square constructs a measure with
extremely powerful properties, some of which we will study in this course.
So let’s eliminate the signs by squaring all the deviations. Then we will take the mean of the squares:
# Step 3. The squared deviations from average

squared_deviations = deviations ** 2
calculation_steps = calculation_steps.with_column(
'Squared Deviations from Average', squared_deviations
)
calculation_steps

Value Deviation from Average Squared Deviations from Average

1 ‑2.75 7.5625
2 ‑1.75 3.0625
2 ‑1.75 3.0625
10 6.25 39.0625
# Step 4. Variance = the mean squared deviation from average

variance = np.mean(squared_deviations)
variance

13.1875

Variance: The mean squared deviation calculated above is called the variance of the values.
While the variance does give us an idea of spread, it is not on the same scale as the original variable as its units are the square of the original. This
makes interpretation very difficult.
So we return to the original scale by taking the positive square root of the variance:
# Step 5.
# Standard Deviation: root mean squared deviation from average
# Steps of calculation: 5 4 3 2 1

sd = variance ** 0.5
sd

3.6314597615834874

14.2.2. Standard Deviation

The quantity that we have just computed is called the standard deviation of the list, and is abbreviated as SD. It measures roughly how far the
numbers on the list are from their average.
Definition. The SD of a list is defined as the root mean square of deviations from average. That’s a mouthful. But read it from right to left and you
have the sequence of steps in the calculation.
Computation. The five steps described above result in the SD. You can also use the function np.std to compute the SD of values in an array:
np.std(any_numbers)

3.6314597615834874

14.2.3. Working with the SD

To see what we can learn from the SD, let’s move to a more interesting dataset than any_numbers. The table nba13 contains data on the players in the
National Basketball Association (NBA) in 2013. For each player, the table records the position at which the player usually played, his height in inches,
his weight in pounds, and his age in years.
nba13 = Table.read_table(path_data + 'nba2013.csv')
nba13

Name Position Height Weight Age in 2013

DeQuan Jones Guard 80 221 23
Darius Miller Guard 80 235 23
Trevor Ariza Guard 80 210 28
James Jones Guard 80 215 32
Wesley Johnson Guard 79 215 26
Klay Thompson Guard 79 205 23
Thabo Sefolosha Guard 79 215 29
Chase Budinger Guard 79 218 25
Kevin Martin Guard 79 185 30
Evan Fournier Guard 79 206 20
... (495 rows omitted)
Here is a histogram of the players’ heights.
nba13.select('Height').hist(bins=np.arange(68, 88, 1))

It is no surprise that NBA players are tall! Their average height is just over 79 inches (6’7”), about 10 inches taller than the average height of men in
the United States.
mean_height = np.mean(nba13.column('Height'))
mean_height

79.06534653465347

About how far off are the players’ heights from the average? This is measured by the SD of the heights, which is about 3.45 inches.
sd_height = np.std(nba13.column('Height'))
sd_height

3.4505971830275546

The towering center Hasheem Thabeet of the Oklahoma City Thunder was the tallest player at a height of 87 inches.
nba13.sort('Height', descending=True).show(3)

Name Position Height Weight Age in 2013

Hasheem Thabeet Center 87 263 26
Roy Hibbert Center 86 278 26
Alex Len Center 85 255 20
... (502 rows omitted)
Thabeet was about 8 inches above the average height.
87 - mean_height

7.934653465346528

That’s a deviation from average, and it is about 2.3 times the standard deviation:
(87 - mean_height)/sd_height

2.2995015194397923

In other words, the height of the tallest player was about 2.3 SDs above average.
At 69 inches tall, Isaiah Thomas was one of the two shortest NBA players in 2013. His height was about 2.9 SDs below average.
nba13.sort('Height').show(3)

Name Position Height Weight Age in 2013

Isaiah Thomas Guard 69 185 24
Nate Robinson Guard 69 180 29
John Lucas III Guard 71 157 30
... (502 rows omitted)
(69 - mean_height)/sd_height

-2.9169868288775844

What we have observed is that the tallest and shortest players were both just a few SDs away from the average height. This is an example of why the
SD is a useful measure of spread. No matter what the shape of the histogram, the average and the SD together tell you a lot about where the
histogram is situated on the number line.

14.2.4. First main reason for measuring spread by the SD

Informal statement. In all numerical data sets, the bulk of the entries are within the range “average $\pm$ a few SDs”.
For now, resist the desire to know exactly what fuzzy words like “bulk” and “few” mean. We wil make them precise later in this section. Let’s just
examine the statement in the context of some more examples.
We have already seen that all of the heights of the NBA players were in the range “average $\pm$ 3 SDs”.
What about the ages? Here is a histogram of the distribution, along with the mean and SD of the ages.
nba13.select('Age in 2013').hist(bins=np.arange(15, 45, 1))

ages = nba13.column('Age in 2013')

mean_age = np.mean(ages)
sd_age = np.std(ages)
mean_age, sd_age

(26.19009900990099, 4.321200441720307)

The average age was just over 26 years, and the SD was about 4.3 years.
How far off were the ages from the average? Just as we did with the heights, let’s look at an example.
Juwan Howard was the oldest player, at 40.
nba13.sort('Age in 2013', descending=True).show(3)

Name Position Height Weight Age in 2013

Juwan Howard Forward 81 250 40
Steve Nash Guard 75 178 39
Derek Fisher Guard 73 210 39
... (502 rows omitted)
Howard’s age was about 3.2 SDs above average.
(40 - mean_age)/sd_age

3.1958482778922357

What we have observed for the heights and ages is true in great generality. For all lists, the bulk of the entries are no more than 2 or 3 SDs away from
the average.

14.2.5. Chebychev’s Bounds

The Russian mathematician Pafnuty Chebychev (1821‑1894) proved a result that makes our rough statements precise.
For all lists, and all numbers $z$, the proportion of entries that are in the range “average $\pm z$ SDs” is at least $1 ‑ \frac{1}{z^2}$.
It is important to note that the result gives a bound, not an exact value or an approximation.
What makes the result powerful is that it is true for all lists – all distributions, no matter how irregular.
Specifically, it says that for every list:
the proportion in the range “average $\pm$ 2 SDs” is at least 1 ‑ 1/4 = 0.75
the proportion in the range “average $\pm$ 3 SDs” is at least 1 ‑ 1/9 $\approx$ 0.89
the proportion in the range “average $\pm$ 4.5 SDs” is at least 1 ‑ 1/$\boldsymbol{4.5^2}$ $\approx$ 0.95
As we noted above, Chebychev’s result gives a lower bound, not an exact answer or an approximation. For example, the percent of entries in the
range “average $\pm ~2$ SDs” might be quite a bit larger than 75%. But it cannot be smaller.

14.2.6. Standard units

In the calculations above, the quantity $z$ measures standard units, the number of standard deviations above average.
Some values of standard units are negative, corresponding to original values that are below average. Other values of standard units are positive. But
no matter what the distribution of the list looks like, Chebychev’s bounds imply that standard units will typically be in the (‑5, 5) range.
To convert a value to standard units, first find how far it is from average, and then compare that deviation with the standard deviation.
\[ z ~=~ \frac{\mbox{value }‑\mbox{ average}}{\mbox{SD}} \]
As we will see, standard units are frequently used in data analysis. So it is useful to define a function that converts an array of numbers to standard
units.
def standard_units(numbers_array):
"Convert any array of numbers to standard units."
return (numbers_array - np.mean(numbers_array))/np.std(numbers_array)

14.2.7. Example
As we saw in an earlier section, the table united contains a column Delay consisting of the departure delay times, in minutes, of over thousands of
United Airlines flights in the summer of 2015. We will create a new column called Delay (Standard Units) by applying the function standard_units
to the column of delay times. This allows us to see all the delay times in minutes as well as their corresponding values in standard units.
united = Table.read_table(path_data + 'united_summer2015.csv')
united = united.with_column(
'Delay (Standard Units)', standard_units(united.column('Delay'))
)
united

Date Flight Number Destination Delay Delay (Standard Units)

6/1/15 73 HNL 257 6.08766
6/1/15 217 EWR 28 0.287279
6/1/15 237 STL ‑3 ‑0.497924
6/1/15 250 SAN 0 ‑0.421937
6/1/15 267 PHL 64 1.19913
6/1/15 273 SEA ‑6 ‑0.573912
6/1/15 278 SEA ‑8 ‑0.62457
6/1/15 292 EWR 12 ‑0.117987
6/1/15 300 HNL 20 0.0846461
6/1/15 317 IND ‑10 ‑0.675228
... (13815 rows omitted)
The standard units that we can see are consistent with what we expect based on Chebychev’s bounds. Most are of quite small size; only one is above
6.
But something rather alarming happens when we sort the delay times from highest to lowest. The standard units that we can see are extremely high!
united.sort('Delay', descending=True)
Date Flight Number Destination Delay Delay (Standard Units)
6/21/15 1964 SEA 580 14.269
6/22/15 300 HNL 537 13.1798
6/21/15 1149 IAD 508 12.4453
6/20/15 353 ORD 505 12.3693
8/23/15 1589 ORD 458 11.1788
7/23/15 1960 LAX 438 10.6722
6/23/15 1606 ORD 430 10.4696
6/4/15 1743 LAX 408 9.91236
6/17/15 1122 HNL 405 9.83637
7/27/15 572 ORD 385 9.32979
... (13815 rows omitted)
What this shows is that it is possible for data to be many SDs above average (and for flights to be delayed by almost 10 hours). The highest value of
delay is more than 14 in standard units.
However, the proportion of these extreme values is small, and Chebychev’s bounds still hold true. For example, let us calculate the percent of delay
times that are in the range “average $\pm$ 3 SDs”. This is the same as the percent of times for which the standard units are in the range (‑3, 3). That
is about 98%, as computed below, consistent with Chebychev’s bound of “at least 89%”.
within_3_sd = united.where('Delay (Standard Units)', are.between(-3, 3))
within_3_sd.num_rows/united.num_rows

0.9790235081374322

The histogram of delay times is shown below, with the horizontal axis in standard units. By the table above, the right hand tail continues all the way
out to $z=14.27$ standard units (580 minutes). The area of the histogram outside the range $z=‑3$ to $z=3$ is about 2%, put together in tiny little
bits that are mostly invisible in the histogram.
united.hist('Delay (Standard Units)', bins=np.arange(-5, 15.5, 0.5))
plots.xticks(np.arange(-6, 17, 3));

14.3. The SD and the Normal Curve

We know that the mean is the balance point of the histogram. Unlike the mean, the SD is usually not easy to identify by looking at the histogram.
However, there is one shape of distribution for which the SD is almost as clearly identifiable as the mean. That is the bell‑shaped disribution. This
section examines that shape, as it appears frequently in probability histograms and also in some histograms of data.

14.3.1. A Roughly Bell‑Shaped Histogram of Data

Let us look at the distribution of heights of mothers in our familiar sample of 1,174 mother‑newborn pairs. The mothers’ heights have a mean of 64
inches and an SD of 2.5 inches. Unlike the heights of the basketball players, the mothers’ heights are distributed fairly symmetrically about the mean
in a bell‑shaped curve.
baby = Table.read_table(path_data + 'baby.csv')

heights = baby.column('Maternal Height')

mean_height = np.round(np.mean(heights), 1)
mean_height

64.0

sd_height = np.round(np.std(heights), 1)
sd_height

2.5

baby.hist('Maternal Height', bins=np.arange(55.5, 72.5, 1), unit='inch')

positions = np.arange(-3, 3.1, 1)*sd_height + mean_height
plots.xticks(positions);

The last two lines of code in the cell above change the labeling of the horizontal axis. Now, the labels correspond to “average $\pm$ $z$ SDs” for $z
= 0, \pm 1, \pm 2$, and $\pm 3$. Because of the shape of the distribution, the “center” has an unambiguous meaning and is clearly visible at 64.

14.3.2. How to Spot the SD on a Bell Shaped Curve

To see how the SD is related to the curve, start at the top of the curve and look towards the right. Notice that there is a place where the curve
changes from looking like an “upside‑down cup” to a “right‑way‑up cup”; formally, the curve has a point of inflection. That point is one SD above
average. It is the point $z=1$, which is “average plus 1 SD” = 66.5 inches.
Symmetrically on the left‑hand side of the mean, the point of inflection is at $z=‑1$, that is, “average minus 1 SD” = 61.5 inches.
In general, for bell‑shaped distributions, the SD is the distance between the mean and the points of inflection on either side.

14.3.3. The standard normal curve

All the bell‑shaped histograms that we have seen look essentially the same apart from the labels on the axes. Indeed, there is really just one basic
curve from which all of these curves can be drawn just by relabeling the axes appropriately.
To draw that basic curve, we will use the units into which we can convert every list: standard units. The resulting curve is therefore called the
standard normal curve.
The standard normal curve has an impressive equation. But for now, it is best to think of it as a smoothed outline of a histogram of a variable that has
been measured in standard units and has a bell‑shaped distribution.
\[ \phi(z) = {\frac{1}{\sqrt{2 \pi}}} e^{‑\frac{1}{2}z^2}, ~~ ‑\infty < z < \infty \]
As always when you examine a new histogram, start by looking at the horizontal axis. On the horizontal axis of the standard normal curve, the values
are standard units.
Here are some properties of the curve. Some are apparent by observation, and others require a considerable amount of mathematics to establish.
The total area under the curve is 1. So you can think of it as a histogram drawn to the density scale.
The curve is symmetric about 0. So if a variable has this distribution, its mean and median are both 0.
The points of inflection of the curve are at ‑1 and +1.
If a variable has this distribution, its SD is 1. The normal curve is one of the very few distributions that has an SD so clearly identifiable on the
histogram.
Since we are thinking of the curve as a smoothed histogram, we will want to represent proportions of the total amount of data by areas under the
curve.
Areas under smooth curves are often found by calculus, using a method called integration. It is a fact of mathematics, however, that the standard
normal curve cannot be integrated in any of the usual ways of calculus.
Therefore, areas under the curve have to be approximated. That is why almost all statistics textbooks carry tables of areas under the normal curve. It
is also why all statistical systems, including a module of Python, include methods that provide excellent approximations to those areas.
from scipy import stats

14.3.4. The standard normal “cdf”

The fundamental function for finding areas under the normal curve is stats.norm.cdf. It takes a numerical argument and returns all the area under
the curve to the left of that number. Formally, it is called the “cumulative distribution function” of the standard normal curve. That rather unwieldy
mouthful is abbreviated as cdf.
Let us use this function to find the area to the left of $z=1$ under the standard normal curve.

The numerical value of the shaded area can be found by calling stats.norm.cdf.
stats.norm.cdf(1)
0.8413447460685429

That’s about 84%. We can now use the symmetry of the curve and the fact that the total area under the curve is 1 to find other areas.
The area to the right of $z=1$ is about 100% ‑ 84% = 16%.

1 - stats.norm.cdf(1)

0.15865525393145707

The area between $z=‑1$ and $z=1$ can be computed in several different ways. It is the gold area under the curve below.

For example, we could calculate the area as “100% ‑ two equal tails”, which works out to roughly 100% ‑ 2x16% = 68%.
Or we could note that the area between $z=1$ and $z=‑1$ is equal to all the area to the left of $z=1$, minus all the area to the left of $z=‑1$.
stats.norm.cdf(1) - stats.norm.cdf(-1)

0.6826894921370859

By a similar calculation, we see that the area between $‑2$ and 2 is about 95%.
stats.norm.cdf(2) - stats.norm.cdf(-2)

0.9544997361036416

In other words, if a histogram is roughly bell shaped, the proportion of data in the range “average $\pm$ 2 SDs” is about 95%.
That is quite a bit more than Chebychev’s lower bound of 75%. Chebychev’s bound is weaker because it has to work for all distributions. If we know
that a distribution is normal, we have good approximations to the proportions, not just bounds.
The table below compares what we know about all distributions and about normal distributions. Notice that when $z=1$, Chebychev’s bound is
correct but not illuminating.
Percent in Range All Distributions: Bound Normal Distribution: Approximation
average $\pm$ 1 SD at least 0% about 68%
average $\pm$ 2 SDs at least 75% about 95%
average $\pm$ 3 SDs at least 88.888…% about 99.73%

14.4. The Central Limit Theorem

Very few of the data histograms that we have seen in this course have been bell shaped. When we have come across a bell shaped distribution, it has
almost invariably been an empirical histogram of a statistic based on a random sample.
The examples below show two very different situations in which an approximate bell shape appears in such histograms.

14.4.1. Net Gain in Roulette

In an earlier section, the bell appeared as the rough shape of the total amount of money we would make if we placed the same bet repeatedly on
different spins of a roulette wheel.
wheel
Pocket Color
0 green
00 green
1 red
2 black
3 red
4 black
5 red
6 black
7 red
8 black
... (28 rows omitted)
Recall that the bet on red pays even money, 1 to 1. We defined the function red_winnings that returns the net winnings on one $1 bet on red.
Specifically, the function takes a color as its argument and returns 1 if the color is red. For all other colors it returns ‑1.
def red_winnings(color):
if color == 'red':
return 1
else:
return -1

The table red shows each pocket’s winnings on red.

red = wheel.with_column(
'Winnings: Red', wheel.apply(red_winnings, 'Color')
)
red

Pocket Color Winnings: Red

0 green ‑1
00 green ‑1
1 red 1
2 black ‑1
3 red 1
4 black ‑1
5 red 1
6 black ‑1
7 red 1
8 black ‑1
... (28 rows omitted)
Your net gain on one bet is one random draw from the Winnings: Red column. There is an 18/38 chance making $1, and a 20/38 chance of making
‑$1. This probability distribution is shown in the histogram below.
red.select('Winnings: Red').hist(bins=np.arange(-1.5, 1.6, 1))
Now suppose you bet many times on red. Your net winnings will be the sum of many draws made at random with replacement from the distribution
above.
It will take a bit of math to list all the possible values of your net winnings along with all of their chances. We won’t do that; instead, we will
approximate the probability distribution by simulation, as we have done all along in this course.
The code below simulates your net gain if you bet $1 on red on 400 different spins of the roulette wheel.
num_bets = 400
repetitions = 10000

net_gain_red = make_array()

for i in np.arange(repetitions):
spins = red.sample(num_bets)
new_net_gain_red = spins.column('Winnings: Red').sum()
net_gain_red = np.append(net_gain_red, new_net_gain_red)

results = Table().with_column(
'Net Gain on Red', net_gain_red
)

results.hist(bins=np.arange(-80, 50, 6))

That’s a roughly bell shaped histogram, even though the distribution we are drawing from is nowhere near bell shaped.
Center. The distribution is centered near ‑20 dollars, roughly. To see why, note that your winnings will be $1 on about 18/38 of the bets, and ‑$1 on
the remaining 20/38. So your average winnings per dollar bet will be roughly ‑5.26 cents:
average_per_bet = 1*(18/38) + (-1)*(20/38)
average_per_bet

-0.05263157894736842

So in 400 bets you expect that your net gain will be about ‑$21:
400 * average_per_bet
-21.052631578947366

For confirmation, we can compute the mean of the 10,000 simulated net gains:
np.mean(results.column(0))

-20.9586

Spread. Run your eye along the curve starting at the center and notice that the point of inflection is near 0. On a bell shaped curve, the SD is the
distance from the center to a point of inflection. The center is roughly ‑$20, which means that the SD of the distribution is around $20.
In the next section we will see where the $20 comes from. For now, let’s confirm our observation by simply calculating the SD of the 10,000 simulated
net gains:
np.std(results.column(0))

20.029115957525438

Summary. The net gain in 400 bets is the sum of the 400 amounts won on each individual bet. The probability distribution of that sum is
approximately normal, with an average and an SD that we can approximate.

14.4.2. Average Flight Delay

The table united contains data on departure delays of 13,825 United Airlines domestic flights out of San Francisco airport in the summer of 2015. As
we have seen before, the distribution of delays has a long right‑hand tail.
united = Table.read_table(path_data + 'united_summer2015.csv')

united.select('Delay').hist(bins=np.arange(-20, 300, 10))

The mean delay was about 16.6 minutes and the SD was about 39.5 minutes. Notice how large the SD is, compared to the mean. Those large
deviations on the right have an effect, even though they are a very small proportion of the data.
mean_delay = np.mean(united.column('Delay'))
sd_delay = np.std(united.column('Delay'))

mean_delay, sd_delay

(16.658155515370705, 39.480199851609314)

Now suppose we sampled 400 delays at random with replacement. You could sample without replacement if you like, but the results would be very
similar to with‑replacement sampling. If you sample a few hundred out of 13,825 without replacement, you hardly change the population each time
you pull out a value.
In the sample, what could the average delay be? We expect it to be around 16 or 17, because that’s the population average; but it is likely to be
somewhat off. Let’s see what we get by sampling. We’ll work with the table delay that only contains the column of delays.
delay = united.select('Delay')

np.mean(delay.sample(400).column('Delay'))

15.59

The sample average varies according to how the sample comes out, so we will simulate the sampling process repeatedly and draw the empirical
histogram of the sample average. That will be an approximation to the probability histogram of the sample average.
sample_size = 400
repetitions = 10000

means = make_array()

for i in np.arange(repetitions):
sample = delay.sample(sample_size)
new_mean = np.mean(sample.column('Delay'))
means = np.append(means, new_mean)

results = Table().with_column(
'Sample Mean', means
)

results.hist(bins=np.arange(10, 25, 0.5))

Once again, we see a rough bell shape, even though we are drawing from a very skewed distribution. The bell is centered somewhere between 16 ad
17, as we expect.

14.4.3. Central Limit Theorem

The reason why the bell shape appears in such settings is a remarkable result of probability theory called the Central Limit Theorem.
The Central Limit Theorem says that the probability distribution of the sum or average of a large random sample drawn with replacement
will be roughly normal, regardless of the distribution of the population from which the sample is drawn.
As we noted when we were studying Chebychev’s bounds, results that can be applied to random samples regardless of the distribution of the
population are very powerful, because in data science we rarely know the distribution of the population.
The Central Limit Theorem makes it possible to make inferences with very little knowledge about the population, provided we have a large random
sample. That is why it is central to the field of statistical inference.

14.4.4. Proportion of Purple Flowers

Recall Mendel’s probability model for the colors of the flowers of a species of pea plant. The model says that the flower colors of the plants are like
draws made at random with replacement from {Purple, Purple, Purple, White}.
In a large sample of plants, about what proportion will have purple flowers? We would expect the answer to be about 0.75, the proportion purple in
the model. And, because proportions are means, the Central Limit Theorem says that the distribution of the sample proportion of purple plants is
roughly normal.
We can confirm this by simulation. Let’s simulate the proportion of purple‑flowered plants in a sample of 200 plants.
colors = make_array('Purple', 'Purple', 'Purple', 'White')

model = Table().with_column('Color', colors)

model

Color
Purple
Purple
Purple
White
props = make_array()

num_plants = 200
repetitions = 10000

for i in np.arange(repetitions):
sample = model.sample(num_plants)
new_prop = np.count_nonzero(sample.column('Color') == 'Purple')/num_plants
props = np.append(props, new_prop)

results = Table().with_column('Sample Proportion: 200', props)

results.hist(bins=np.arange(0.65, 0.85, 0.01))

There’s that normal curve again, as predicted by the Central Limit Theorem, centered at around 0.75 just as you would expect.
How would this distribution change if we increased the sample size? Let’s run the code again with a sample size of 800, and collect the results of
simulations in the same table in which we collected simulations based on a sample size of 200. We will keep the number of repetitions the same as
before so that the two columns have the same length.
props2 = make_array()

num_plants = 800

for i in np.arange(repetitions):
sample = model.sample(num_plants)
new_prop = np.count_nonzero(sample.column('Color') == 'Purple')/num_plants
props2 = np.append(props2, new_prop)

results = results.with_column('Sample Proportion: 800', props2)

results.hist(bins=np.arange(0.65, 0.85, 0.01))

Both distributions are approximately normal but one is narrower than the other. The proportions based on a sample size of 800 are more tightly
clustered around 0.75 than those from a sample size of 200. Increasing the sample size has decreased the variability in the sample proportion.
This should not be surprising. We have leaned many times on the intuition that a larger sample size generally reduces the variability of a statistic.
However, in the case of a sample average, we can quantify the relationship between sample size and variability.
Exactly how does the sample size affect the variability of a sample average or proportion? That is the question we will examine in the next section.

14.5. The Variability of the Sample Mean

By the Central Limit Theorem, the probability distribution of the mean of a large random sample is roughly normal. The bell curve is centered at the
population mean. Some of the sample means are higher, and some lower, but the deviations from the population mean are roughly symmetric on
either side, as we have seen repeatedly. Formally, probability theory shows that the sample mean is an unbiased estimate of the population mean.
In our simulations, we also noticed that the means of larger samples tend to be more tightly clustered around the population mean than means of
smaller samples. In this section, we will quantify the variability of the sample mean and develop a relation between the variability and the sample size.
Let’s start with our table of flight delays. The mean delay is about 16.7 minutes, and the distribution of delays is skewed to the right.
united = Table.read_table(path_data + 'united_summer2015.csv')
delay = united.select('Delay')

pop_mean = np.mean(delay.column('Delay'))
pop_mean

16.658155515370705

Now let’s take random samples and look at the probability distribution of the sample mean. As usual, we will use simulation to get an empirical
approximation to this distribution.
We will define a function simulate_sample_mean to do this, because we are going to vary the sample size later. The arguments are the name of the
table, the label of the column containing the variable, the sample size, and the number of simulations.
"""Empirical distribution of random sample means"""

def simulate_sample_mean(table, label, sample_size, repetitions):

means = make_array()

for i in range(repetitions):
new_sample = table.sample(sample_size)
new_sample_mean = np.mean(new_sample.column(label))
means = np.append(means, new_sample_mean)

sample_means = Table().with_column('Sample Means', means)

# Display empirical histogram and print all relevant quantities

sample_means.hist(bins=20)
plots.xlabel('Sample Means')
plots.title('Sample Size ' + str(sample_size))
print("Sample size: ", sample_size)
print("Population mean:", np.mean(table.column(label)))
print("Average of sample means: ", np.mean(means))
print("Population SD:", np.std(table.column(label)))
print("SD of sample means:", np.std(means))

Let us simulate the mean of a random sample of 100 delays, then of 400 delays, and finally of 625 delays. We will perform 10,000 repetitions of each
of these process. The xlim and ylim lines set the axes consistently in all the plots for ease of comparison. You can just ignore those two lines of code
in each cell.
simulate_sample_mean(delay, 'Delay', 100, 10000)
plots.xlim(5, 35)
plots.ylim(0, 0.25);

Sample size: 100

Population mean: 16.658155515370705
Average of sample means: 16.672836
Population SD: 39.480199851609314
SD of sample means: 3.92467202924066

simulate_sample_mean(delay, 'Delay', 400, 10000)

plots.xlim(5, 35)
plots.ylim(0, 0.25);
Sample size: 400
Population mean: 16.658155515370705
Average of sample means: 16.678091499999997
Population SD: 39.480199851609314
SD of sample means: 1.9474592014668113

simulate_sample_mean(delay, 'Delay', 625, 10000)

plots.xlim(5, 35)
plots.ylim(0, 0.25);

Sample size: 625

Population mean: 16.658155515370705
Average of sample means: 16.649224
Population SD: 39.480199851609314
SD of sample means: 1.5883338034053167

You can see the Central Limit Theorem in action – the histograms of the sample means are roughly normal, even though the histogram of the delays
themselves is far from normal.
You can also see that each of the three histograms of the sample means is centered very close to the population mean. In each case, the “average of
sample means” is very close to 16.66 minutes, the population mean. Both values are provided in the printout above each histogram. As expected, the
sample mean is an unbiased estimate of the population mean.

14.5.1. The SD of All the Sample Means

You can also see that the histograms get narrower, and hence taller, as the sample size increases. We have seen that before, but now we will pay
closer attention to the measure of spread.
The SD of the population of all delays is about 40 minutes.
pop_sd = np.std(delay.column('Delay'))
pop_sd

39.480199851609314

Take a look at the SDs in the sample mean histograms above. In all three of them, the SD of the population of delays is about 40 minutes, because all
the samples were taken from the same population.
Now look at the SD of all 10,000 sample means, when the sample size is 100. That SD is about one‑tenth of the population SD. When the sample size
is 400, the SD of all the sample means is about one‑twentieth of the population SD. When the sample size is 625, the SD of the sample means is
about one‑twentyfifth of the population SD.
It seems like a good idea to compare the SD of the empirical distribution of the sample means to the quantity “population SD divided by the square
root of the sample size.”
Here are the numerical values. For each sample size in the first column, 10,000 random samples of that size were drawn, and the 10,000 sample
means were calculated. The second column contains the SD of those 10,000 sample means. The third column contains the result of the calculation
“population SD divided by the square root of the sample size.”
The cell takes a while to run, as it’s a large simulation. But you’ll soon see that it’s worth the wait.
repetitions = 10000
sample_sizes = np.arange(25, 626, 25)

sd_means = make_array()

for n in sample_sizes:
means = make_array()
for i in np.arange(repetitions):
means = np.append(means, np.mean(delay.sample(n).column('Delay')))
sd_means = np.append(sd_means, np.std(means))

sd_comparison = Table().with_columns(
'Sample Size n', sample_sizes,
'SD of 10,000 Sample Means', sd_means,
'pop_sd/sqrt(n)', pop_sd/np.sqrt(sample_sizes)
)

sd_comparison

Sample Size n SD of 10,000 Sample Means pop_sd/sqrt(n)

25 7.94482 7.89604
50 5.6131 5.58334
75 4.57417 4.55878
100 3.98687 3.94802
125 3.49769 3.53122
150 3.22776 3.22354
175 3.00675 2.98442
200 2.77764 2.79167
225 2.64268 2.63201
250 2.49447 2.49695
... (15 rows omitted)
The values in the second and third columns are very close. If we plot each of those columns with the sample size on the horizontal axis, the two
graphs are essentially indistinguishable.
sd_comparison.plot('Sample Size n')
There really are two curves there. But they are so close to each other that it looks as though there is just one.
What we are seeing is an instance of a general result. Remember that the graph above is based on 10,000 replications for each sample size. But there
are many more than 10,000 samples of each size. The probability distribution of the sample mean is based on the means of all possible samples of a
fixed size.
Fix a sample size. If the samples are drawn at random with replacement from the population, then
\[ {\mbox{SD of all possible sample means}} ~=~ \frac{\mbox{Population SD}}{\sqrt{\mbox{sample size}}} \]
This is the standard deviation of the averages of all the possible samples that could be drawn. It measures roughly how far off the sample means
are from the population mean.

14.5.2. The Central Limit Theorem for the Sample Mean

If you draw a large random sample with replacement from a population, then, regardless of the distribution of the population, the probability
distribution of the sample mean is roughly normal, centered at the population mean, with an SD equal to the population SD divided by the square root
of the sample size.

14.5.3. The Accuracy of the Sample Mean

The SD of all possible sample means measures how variable the sample mean can be. As such, it is taken as a measure of the accuracy of the sample
mean as an estimate of the population mean. The smaller the SD, the more accurate the estimate.
The formula shows that:
The population size doesn’t affect the accuracy of the sample mean. The population size doesn’t appear anywhere in the formula.
The population SD is a constant; it’s the same for every sample drawn from the population. The sample size can be varied. Because the sample
size appears in the denominator, the variability of the sample mean decreases as the sample size increases, and hence the accuracy increases.

14.5.4. The Square Root Law

From the table of SD comparisons, you can see that the SD of the means of random samples of 25 flight delays is about 8 minutes. If you multiply the
sample size by 4, you’ll get samples of size 100. The SD of the means of all of those samples is about 4 minutes. That’s smaller than 8 minutes, but
it’s not 4 times as small; it’s only 2 times as small. That’s because the sample size in the denominator has a square root over it. The sample size
increased by a factor of 4, but the SD went down by a factor of $2 = \sqrt{4}$. In other words, the accuracy went up by a factor of $2 = \sqrt{4}$.
In general, when you multiply the sample size by a factor, the accuracy of the sample mean goes up by the square root of that factor.
So to increase accuracy by a factor of 10, you have to multiply sample size by a factor of 100. Accuracy doesn’t come cheap!

14.6. Choosing a Sample Size

Candidate A is contesting an election. A polling organization wants to estimate the proportion of voters who will vote for her. Let’s suppose that they
plan to take a simple random sample of voters, though in reality their method of sampling would be more complex. How can they decide how large
their sample should be, to get a desired level of accuracy?
We are now in a position to answer this question, after making a few assumptions:
The population of voters is very large and that therefore we can just as well assume that the random sample will be drawn with replacement.
The polling organization will make its estimate by constructing an approximate 95% confidence interval for the percent of voters who will vote
for Candidate A.
The desired level of accuracy is that the width of the interval should be no more than 1%. That’s pretty accurate! For example, the confidence
interval (33.2%, 34%) would be fine but (33.2%, 35%) would not.
We will work with the sample proportion of voters for Candidate A. Recall that a proportion is a mean, when the values in the population are only 0
(the type of individual you are not counting) or 1 (the type of individual you are counting).

14.6.1. Width of Confidence Interval

If we had a random sample, we could go about using the bootstrap to construct a confidence interval for the percent of voters for Candidate A. But
we don’t have a sample yet – we are trying to find out how big the sample has to be so that our confidence interval is as narrow as we want it to be.
In situations like this, it helps to see what theory predicts.
The Central Limit Theorem says that the probabilities for the sample proportion are roughly normally distributed, centered at the population
proportion of 1’s, with an SD equal to the SD of the population of 0’s and 1’s divided by the square root of the sample size.
So the confidence interval will still be the “middle 95%” of a normal distribution, even though we can’t pick off the ends as the 2.5th and 97.5th
percentiles of bootstrapped proportions.
Is there another way to find how wide the interval would be? Yes, because we know that for normally distributed variables, the interval “center $\pm$
2 SDs” contains 95% of the data.
The confidence interval will stretch for 2 SDs of the sample proportion, on either side of the center. So the width of the interval will be 4 SDs of the
sample proportion.
We are willing to tolerate a width of 1% = 0.01. So, using the formula developed in the last section,
\[ 4 \times \frac{\mbox{SD of the 0‑1 population}}{\sqrt{\mbox{sample size}}} ~ \le ~ 0.01 \]
So
\[ \sqrt{\mbox{sample size}} ~ \ge ~ 4 \times \frac{\mbox{SD of the 0‑1 population}}{0.01} \]

14.6.2. The SD of a collection of 0’s and 1’s

If we knew the SD of the population, we’d be done. We could calculate the square root of the sample size, and then take the square to get the sample
size. But we don’t know the SD of the population. The population consists of 1 for each voter for Candidate A, and 0 for all other voters, and we don’t
know what proportion of each kind there are. That’s what we’re trying to estimate.
So are we stuck? No, because we can bound the SD of the population. Here are histograms of two such distributions, one for an equal proportion of
1’s and 0’s, and one with 90% 1’s and 10% 0’s. Which one has the bigger SD?

Remember that the possible values in the population are only 0 and 1.
The blue histogram (50% 1’s and 50% 0’s) has more spread than the gold. The mean is 0.5. Half the deviations from mean are equal to 0.5 and the
other half equal to ‑0.5, so the SD is 0.5.
In the gold histogram, all of the area is being squished up around 1, leading to less spread. 90% of the deviations are small: 0.1. The other 10% are
‑0.9 which is large, but overall the spread is smaller than in the blue histogram.
The same observation would hold if we varied the proportion of 1’s or let the proportion of 0’s be larger than the proportion of 1’s. Let’s check this by
calculating the SDs of populations of 10 elements that only consist of 0’s and 1’s, in varying proportions. The function np.ones is useful for this. It
takes a positive integer as its argument and returns an array consisting of that many 1’s.
sd = make_array()
for i in np.arange(1, 10, 1):
# Create an array of i 1's and (10-i) 0's
population = np.append(np.ones(i), 1-np.ones(10-i))
sd = np.append(sd, np.std(population))

zero_one_sds = Table().with_columns(
"Population Proportion of 1's", np.arange(0.1, 1, 0.1),
"Population SD", sd
)

zero_one_sds

Population Proportion of 1's Population SD

0.1 0.3
0.2 0.4
0.3 0.458258
0.4 0.489898
0.5 0.5
0.6 0.489898
0.7 0.458258
0.8 0.4
0.9 0.3
Not surprisingly, the SD of a population with 10% 1’s and 90% 0’s is the same as that of a population with 90% 1’s and 10% 0’s. That’s because you
switch the bars of one histogram to get the other; there is no change in spread.
More importantly for our purposes, the SD increases as the proportion of 1’s increases, until the proportion of 1’s is 0.5; then it starts to decrease
symmetrically.
zero_one_sds.scatter("Population Proportion of 1's")

Summary: The SD of a population of 1’s and 0’s is at most 0.5. That’s the value of the SD when 50% of the population is coded 1 and the other 50%
are coded 0.

14.6.3. The Sample Size

We know that
\[ \sqrt{\mbox{sample size}} ~ \ge ~ 4 \times \frac{\mbox{SD of the 0‑1 population}}{0.01} \]
and that the SD of the 0‑1 population is at most 0.5, regardless of the proportion of 1’s in the population. So it is safe to take
\[ \sqrt{\mbox{sample size}} ~ \ge ~ 4 \times \frac{0.5}{0.01} ~=~ 200 \]
So the sample size should be at least $200^2 = 40,000$. That’s an enormous sample! But that’s what you need if you want to guarantee great
accuracy with high confidence no matter what the population looks like.

15. Prediction
An important aspect of data science is to find out what data can tell us about the future. What do data about climate and pollution say about
temperatures a few decades from now? Based on a person’s internet profile, which websites are likely to interest them? How can a patient’s medical
history be used to judge how well he or she will respond to a treatment?
To answer such questions, data scientists have developed methods for making predictions. In this chapter we will study one of the most commonly
used ways of predicting the value of one variable based on the value of another.
Here is a historical dataset used for the prediction of the heights of adults based on the heights of their parents. We have studied this dataset in an
earlier section. The table heights contains data on the midparent height and child’s height (all in inches) for a population of 934 adult “children”.
Recall that the midparent height is an average of the heights of the two parents.
# Data on heights of parents and their adult children
original = Table.read_table(path_data + 'family_heights.csv')
heights = Table().with_columns(
'MidParent', original.column('midparentHeight'),
'Child', original.column('childHeight')
)

heights

MidParent Child
75.43 73.2
75.43 69.2
75.43 69
75.43 69
73.66 73.5
73.66 72.5
73.66 65.5
73.66 65.5
72.06 71
72.06 68
... (924 rows omitted)
heights.scatter('MidParent')
A primary reason for studying the data was to be able to predict the adult height of a child born to parents who were similar to those in the dataset.
We made these predictions in Section 8.1, after noticing the positive association between the two variables.
Our approach was to base the prediction on all the points that correspond to a midparent height of around the midparent height of the new person.
To do this, we wrote a function called predict_child which takes a midparent height as its argument and returns the average height of all the
children who had midparent heights within half an inch of the argument.
def predict_child(mpht):
"""Return a prediction of the height of a child
whose parents have a midparent height of mpht.

The prediction is the average height of the children

whose midparent height is in the range mpht plus or minus 0.5 inches.
"""

close_points = heights.where('MidParent', are.between(mpht-0.5, mpht + 0.5))

return close_points.column('Child').mean()

We applied the function to the column of Midparent heights, and visualized the result.
# Apply predict_child to all the midparent heights

heights_with_predictions = heights.with_column(
'Prediction', heights.apply(predict_child, 'MidParent')
)

# Draw the original scatter plot along with the predicted values

heights_with_predictions.scatter('MidParent')

The prediction at a given midparent height lies roughly at the center of the vertical strip of points at the given height. This method of prediction is
called regression. Later in this chapter we will see whether we can avoid our arbitrary definitions of “closeness” being “within 0.5 inches”. But first we
will develop a measure that can be used in many settings to decide how good one variable will be as a predictor of another.

15.1. Correlation
In this section we will develop a measure of how tightly clustered a scatter diagram is about a straight line. Formally, this is called measuring linear
association.
The table hybrid contains data on hybrid passenger cars sold in the United States from 1997 to 2013. The data were adapted from the online data
archive of Prof. Larry Winner of the University of Florida. The columns:
vehicle: model of the car
year: year of manufacture
msrp: manufacturer’s suggested retail price in 2013 dollars
acceleration: acceleration rate in km per hour per second
mpg: fuel econonmy in miles per gallon
class: the model’s class.
hybrid = Table.read_table(path_data + 'hybrid.csv')

hybrid

vehicle year msrp acceleration mpg class

Prius (1st Gen) 1997 24509.7 7.46 41.26 Compact
Tino 2000 35355 8.2 54.1 Compact
Prius (2nd Gen) 2000 26832.2 7.97 45.23 Compact
Insight 2000 18936.4 9.52 53 Two Seater
Civic (1st Gen) 2001 25833.4 7.04 47.04 Compact
Insight 2001 19036.7 9.52 53 Two Seater
Insight 2002 19137 9.71 53 Two Seater
Alphard 2003 38084.8 8.33 40.46 Minivan
Insight 2003 19137 9.52 53 Two Seater
Civic 2003 14071.9 8.62 41 Compact
... (143 rows omitted)
The graph below is a scatter plot of msrp versus acceleration. That means msrp is plotted on the vertical axis and accelaration on the horizontal.
hybrid.scatter('acceleration', 'msrp')

Notice the positive association. The scatter of points is sloping upwards, indicating that cars with greater acceleration tended to cost more, on
average; conversely, the cars that cost more tended to have greater acceleration on average.
The scatter diagram of MSRP versus mileage shows a negative association. Hybrid cars with higher mileage tended to cost less, on average. This
seems surprising till you consider that cars that accelerate fast tend to be less fuel efficient and have lower mileage. As the previous scatter plot
showed, those were also the cars that tended to cost more.
hybrid.scatter('mpg', 'msrp')
Along with the negative association, the scatter diagram of price versus efficiency shows a non‑linear relation between the two variables. The points
appear to be clustered around a curve, not around a straight line.
If we restrict the data just to the SUV class, however, the association between price and efficiency is still negative but the relation appears to be more
linear. The relation between the price and acceleration of SUV’s also shows a linear trend, but with a positive slope.
suv = hybrid.where('class', 'SUV')
suv.scatter('mpg', 'msrp')

suv.scatter('acceleration', 'msrp')

You will have noticed that we can derive useful information from the general orientation and shape of a scatter diagram even without paying attention
to the units in which the variables were measured.
Indeed, we could plot all the variables in standard units and the plots would look the same. This gives us a way to compare the degree of linearity in
two scatter diagrams.
Recall that in an earlier section we defined the function standard_units to convert an array of numbers to standard units.
def standard_units(any_numbers):
"Convert any array of numbers to standard units."
return (any_numbers - np.mean(any_numbers))/np.std(any_numbers)

We can use this function to re‑draw the two scatter diagrams for SUVs, with all the variables measured in standard units.
Table().with_columns(
'mpg (standard units)', standard_units(suv.column('mpg')),
'msrp (standard units)', standard_units(suv.column('msrp'))
).scatter(0, 1)
plots.xlim(-3, 3)
plots.ylim(-3, 3);

Table().with_columns(
'acceleration (standard units)', standard_units(suv.column('acceleration')),
'msrp (standard units)', standard_units(suv.column('msrp'))
).scatter(0, 1)
plots.xlim(-3, 3)
plots.ylim(-3, 3);

The associations that we see in these figures are the same as those we saw before. Also, because the two scatter diagrams are now drawn on exactly
the same scale, we can see that the linear relation in the second diagram is a little more fuzzy than in the first.
We will now define a measure that uses standard units to quantify the kinds of association that we have seen.

15.1.1. The correlation coefficient

The correlation coefficient measures the strength of the linear relationship between two variables. Graphically, it measures how clustered the scatter
diagram is around a straight line.
The term correlation coefficient isn’t easy to say, so it is usually shortened to correlation and denoted by $r$.
Here are some mathematical facts about $r$ that we will just observe by simulation.
The correlation coefficient $r$ is a number between $‑1$ and 1.
$r$ measures the extent to which the scatter plot clusters around a straight line.
$r = 1$ if the scatter diagram is a perfect straight line sloping upwards, and $r = ‑1$ if the scatter diagram is a perfect straight line sloping
downwards.
The function r_scatter takes a value of $r$ as its argument and simulates a scatter plot with a correlation very close to $r$. Because of randomness
in the simulation, the correlation is not expected to be exactly equal to $r$.
Call r_scatter a few times, with different values of $r$ as the argument, and see how the scatter plot changes.
When $r=1$ the scatter plot is perfectly linear and slopes upward. When $r=‑1$, the scatter plot is perfectly linear and slopes downward. When \
(r=0\), the scatter plot is a formless cloud around the horizontal axis, and the variables are said to be uncorrelated.
r_scatter(0.9)

r_scatter(0.25)

r_scatter(0)
r_scatter(-0.55)

15.1.2. Calculating $r$

The formula for $r$ is not apparent from our observations so far. It has a mathematical basis that is outside the scope of this class. However, as you
will see, the calculation is straightforward and helps us understand several of the properties of $r$.
Formula for $r$:
$r$ is the average of the products of the two variables, when both variables are measured in standard units.
Here are the steps in the calculation. We will apply the steps to a simple table of values of $x$ and $y$.
x = np.arange(1, 7, 1)
y = make_array(2, 3, 1, 5, 2, 7)
t = Table().with_columns(
'x', x,
'y', y
)
t

x y
1 2
2 3
3 1
4 5
5 2
6 7
Based on the scatter diagram, we expect that $r$ will be positive but not equal to 1.
t.scatter(0, 1, s=30, color='red')

Step 1. Convert each variable to standard units.

t_su = t.with_columns(
'x (standard units)', standard_units(x),
'y (standard units)', standard_units(y)
)
t_su

x y x (standard units) y (standard units)

1 2 ‑1.46385 ‑0.648886
2 3 ‑0.87831 ‑0.162221
3 1 ‑0.29277 ‑1.13555
4 5 0.29277 0.811107
5 2 0.87831 ‑0.648886
6 7 1.46385 1.78444
Step 2. Multiply each pair of standard units.
t_product = t_su.with_column('product of standard units', t_su.column(2) *
t_su.column(3))
t_product

x y x (standard units) y (standard units) product of standard units

1 2 ‑1.46385 ‑0.648886 0.949871
2 3 ‑0.87831 ‑0.162221 0.142481
3 1 ‑0.29277 ‑1.13555 0.332455
4 5 0.29277 0.811107 0.237468
5 2 0.87831 ‑0.648886 ‑0.569923
6 7 1.46385 1.78444 2.61215
Step 3. $r$ is the average of the products computed in Step 2.
# r is the average of the products of standard units

r = np.mean(t_product.column(4))
r

0.6174163971897709

As expected, $r$ is positive but not equal to 1.

15.1.3. Properties of $r$
The calculation shows that:
$r$ is a pure number. It has no units. This is because $r$ is based on standard units.
$r$ is unaffected by changing the units on either axis. This too is because $r$ is based on standard units.
$r$ is unaffected by switching the axes. Algebraically, this is because the product of standard units does not depend on which variable is called
$x$ and which $y$. Geometrically, switching axes reflects the scatter plot about the line $y=x$, but does not change the amount of clustering
nor the sign of the association.
t.scatter('y', 'x', s=30, color='red')

15.1.4. The correlation function

We are going to be calculating correlations repeatedly, so it will help to define a function that computes it by performing all the steps described
above. Let’s define a function correlation that takes a table and the labels of two columns in the table. The function returns $r$, the mean of the
products of those column values in standard units.
def correlation(t, x, y):
return np.mean(standard_units(t.column(x))*standard_units(t.column(y)))

Let’s call the function on the x and y columns of t. The function returns the same answer to the correlation between $x$ and $y$ as we got by direct
application of the formula for $r$.
correlation(t, 'x', 'y')

0.6174163971897709

As we noticed, the order in which the variables are specified doesn’t matter.
correlation(t, 'y', 'x')

0.6174163971897709

Calling correlation on columns of the table suv gives us the correlation between price and mileage as well as the correlation between price and
acceleration.
correlation(suv, 'mpg', 'msrp')

-0.6667143635709919

correlation(suv, 'acceleration', 'msrp')

0.48699799279959155

These values confirm what we had observed:

There is a negative association between price and efficiency, whereas the association between price and acceleration is positive.
The linear relation between price and acceleration is a little weaker (correlation about 0.5) than between price and mileage (correlation about
‑0.67).
Correlation is a simple and powerful concept, but it is sometimes misused. Before using $r$, it is important to be aware of what correlation does and
does not measure.

15.1.5. Association is not Causation

Correlation only measures association. Correlation does not imply causation. Though the correlation between the weight and the math ability of
children in a school district may be positive, that does not mean that doing math makes children heavier or that putting on weight improves the
children’s math skills. Age is a confounding variable: older children are both heavier and better at math than younger children, on average.

15.1.6. Correlation Measures Linear Association

Correlation measures only one kind of association – linear. Variables that have strong non‑linear association might have very low correlation. Here is
an example of variables that have a perfect quadratic relation $y = x^2$ but have correlation equal to 0.
new_x = np.arange(-4, 4.1, 0.5)
nonlinear = Table().with_columns(
'x', new_x,
'y', new_x**2
)
nonlinear.scatter('x', 'y', s=30, color='r')

correlation(nonlinear, 'x', 'y')

0.0

15.1.7. Correlation is Affected by Outliers

Outliers can have a big effect on correlation. Here is an example where a scatter plot for which $r$ is equal to 1 is turned into a plot for which $r$ is
equal to 0, by the addition of just one outlying point.
line = Table().with_columns(
'x', make_array(1, 2, 3, 4),
'y', make_array(1, 2, 3, 4)
)
line.scatter('x', 'y', s=30, color='r')
correlation(line, 'x', 'y')

1.0

outlier = Table().with_columns(
'x', make_array(1, 2, 3, 4, 5),
'y', make_array(1, 2, 3, 4, 0)
)
outlier.scatter('x', 'y', s=30, color='r')

correlation(outlier, 'x', 'y')

0.0

15.1.8. Ecological Correlations Should be Interpreted with Care

Correlations based on aggregated data can be misleading. As an example, here are data on the Critical Reading and Math SAT scores in 2014. There
is one point for each of the 50 states and one for Washington, D.C. The column Participation Rate contains the percent of high school seniors who
took the test. The next three columns show the average score in the state on each portion of the test, and the final column is the average of the total
scores on the test.
sat2014 = Table.read_table(path_data + 'sat2014.csv').sort('State')
sat2014
State Participation Rate Critical Reading Math Writing Combined
Alabama 6.7 547 538 532 1617
Alaska 54.2 507 503 475 1485
Arizona 36.4 522 525 500 1547
Arkansas 4.2 573 571 554 1698
California 60.3 498 510 496 1504
Colorado 14.3 582 586 567 1735
Connecticut 88.4 507 510 508 1525
Delaware 100 456 459 444 1359
District of Columbia 100 440 438 431 1309
Florida 72.2 491 485 472 1448
... (41 rows omitted)
The scatter diagram of Math scores versus Critical Reading scores is very tightly clustered around a straight line; the correlation is close to 0.985.
sat2014.scatter('Critical Reading', 'Math')

correlation(sat2014, 'Critical Reading', 'Math')

0.9847558411067434

That’s an extremely high correlation. But it’s important to note that this does not reflect the strength of the relation between the Math and Critical
Reading scores of students.
The data consist of average scores in each state. But states don’t take tests – students do. The data in the table have been created by lumping all the
students in each state into a single point at the average values of the two variables in that state. But not all students in the state will be at that point,
as students vary in their performance. If you plot a point for each student instead of just one for each state, there will be a cloud of points around
each point in the figure above. The overall picture will be more fuzzy. The correlation between the Math and Critical Reading scores of the students
will be lower than the value calculated based on state averages.
Correlations based on aggregates and averages are called ecological correlations and are frequently reported. As we have just seen, they must be
interpreted with care.

15.1.9. Serious or tongue‑in‑cheek?

In 2012, a paper in the respected New England Journal of Medicine examined the relation between chocolate consumption and Nobel Prizes in a
group of countries. The Scientific American responded seriously whereas others were more relaxed. You are welcome to make your own decision!
The following graph, provided in the paper, should motivate you to go and take a look.
15.2. The Regression Line
The correlation coefficient $r$ doesn’t just measure how clustered the points in a scatter plot are about a straight line. It also helps identify the
straight line about which the points are clustered. In this section we will retrace the path that Galton and Pearson took to discover that line.
As we have seen, our dataset on the heights of parents and their adult children indicates a linear association between the two variables. The linearity
was confirmed when our predictions of the children’s heights based on the midparent heights roughly followed a straight line.
original = Table.read_table(path_data + 'family_heights.csv')

heights = Table().with_columns(
'MidParent', original.column('midparentHeight'),
'Child', original.column('childHeight')
)

def predict_child(mpht):
"""Return a prediction of the height of a child
whose parents have a midparent height of mpht.

The prediction is the average height of the children

whose midparent height is in the range mpht plus or minus 0.5 inches.
"""

close_points = heights.where('MidParent', are.between(mpht-0.5, mpht + 0.5))

return close_points.column('Child').mean()

heights_with_predictions = heights.with_column(
'Prediction', heights.apply(predict_child, 'MidParent')
)

heights_with_predictions.scatter('MidParent')
15.2.1. Measuring in Standard Units
Let’s see if we can find a way to identify this line. First, notice that linear association doesn’t depend on the units of measurement – we might as well
measure both variables in standard units.
def standard_units(xyz):
"Convert any array of numbers to standard units."
return (xyz - np.mean(xyz))/np.std(xyz)

heights_SU = Table().with_columns(
'MidParent SU', standard_units(heights.column('MidParent')),
'Child SU', standard_units(heights.column('Child'))
)
heights_SU

MidParent SU Child SU
3.45465 1.80416
3.45465 0.686005
3.45465 0.630097
3.45465 0.630097
2.47209 1.88802
2.47209 1.60848
2.47209 ‑0.348285
2.47209 ‑0.348285
1.58389 1.18917
1.58389 0.350559
... (924 rows omitted)
On this scale, we can calculate our predictions exactly as before. But first we have to figure out how to convert our old definition of “close” points to a
value on the new scale. We had said that midparent heights were “close” if they were within 0.5 inches of each other. Since standard units measure
distances in units of SDs, we have to figure out how many SDs of midparent height correspond to 0.5 inches.
One SD of midparent heights is about 1.8 inches. So 0.5 inches is about 0.28 SDs.
sd_midparent = np.std(heights.column(0))
sd_midparent

1.8014050969207571

0.5/sd_midparent
0.277561110965367

We are now ready to modify our prediction function to make predictions on the standard units scale. All that has changed is that we are using the
table of values in standard units, and defining “close” as above.
def predict_child_su(mpht_su):
"""Return a prediction of the height (in standard units) of a child
whose parents have a midparent height of mpht_su in standard units.
"""
close = 0.5/sd_midparent
close_points = heights_SU.where('MidParent SU', are.between(mpht_su-close, mpht_su +
close))
return close_points.column('Child SU').mean()

heights_with_su_predictions = heights_SU.with_column(
'Prediction SU', heights_SU.apply(predict_child_su, 'MidParent SU')
)

heights_with_su_predictions.scatter('MidParent SU')

This plot looks exactly like the plot drawn on the original scale. Only the numbers on the axes have changed. This confirms that we can understand
the prediction process by just working in standard units.

15.2.2. Identifying the Line in Standard Units

The scatter plot above has a football shape – that is, it is roughly oval like an American football. Not all scatter plots are football shaped, not even
those that show linear association. But in this section we will work only with football shaped scatter plots. In the next section, we will generalize our
analysis to other shapes of plots.
Here is a football shaped scatter plot with both variables measured in standard units. The 45 degree line is shown in red.
But the 45 degree line is not the line that picks off the centers of the vertical strips. You can see that in the figure below, where the vertical line at 1.5
standard units is shown in black. The points on the scatter plot near the black line all have heights roughly in the ‑2 to 3 range. The red line is too high
to pick off the center.

So the 45 degree line is not the “graph of averages.” That line is the green one shown below.

Both lines go through the origin (0, 0). The green line goes through the centers of the vertical strips (at least roughly), and is flatter than the red 45
degree line.
The slope of the 45 degree line is 1. So the slope of the green “graph of averages” line is a value that is positive but less than 1.
What value could that be? You’ve guessed it – it’s $r$.

15.2.3. The Regression Line, in Standard Units

The green “graph of averages” line is called the regression line, for a reason that we will explain shortly. But first, let’s simulate some football shaped
scatter plots with different values of $r$, and see how the line changes. In each case, the red 45 degree line has been drawn for comparison.
The function that performs the simulation is called regression_line and takes $r$ as its argument.
regression_line(0.95)
regression_line(0.6)

When $r$ is close to 1, the scatter plot, the 45 degree line, and the regression line are all very close to each other. But for more moderate values of \
(r\), the regression line is noticeably flatter.

15.2.4. The Regression Effect

In terms of prediction, this means that for a parents whose midparent height is at 1.5 standard units, our prediction of the child’s height is somewhat
less than 1.5 standard units. If the midparent height is 2 standard units, we predict that the child’s height will be somewhat less than 2 standard units.
In other words, we predict that the child will be somewhat closer to average than the parents were. This is called “regression to the mean” and it is
how the name regression arises.
Regression to the mean also works when the midparent height is below average. Children whose midparent heights were below average turned out to
be somewhat taller relative to their generation, on average.
In general, individuals who are away from average on one variable are expected to be not quite as far away from average on the other. This is called
the regression effect.
Keep in mind that the regression effect is a statement about averages. For example, it says that if you take all children whose midparent height is 1.5
standard units, then the average height of these children is somewhat less than 1.5 standard units. It doesn’t say that all of these children will be
somewhat less than 1.5 standard units in height. Some will be taller, and some will be shorter. The average of these heights will be less than 1.5
standard units.

15.2.5. The Equation of the Regression Line

In regression, we use the value of one variable (which we will call $x$) to predict the value of another (which we will call $y$). When the variables \
(x\) and $y$ are measured in standard units, the regression line for predicting $y$ based on $x$ has slope $r$ and passes through the origin. Thus
the equation of the regression line can be written as:
\[ \mbox{estimate of }y ~=~ r \cdot x ~~~ \mbox{when both variables are measured in standard units} \]
In the original units of the data, this becomes
\[ \frac{\mbox{estimate of}~y ~‑~\mbox{average of}~y}{\mbox{SD of}~y} ~=~ r \times \frac{\mbox{the given}~x ~‑~\mbox{average of}~x}{\mbox{SD
of}~x} \]

The slope and intercept of the regression line in original units can be derived from the diagram above.
\[\[ \mathbf{\mbox{slope of the
\mathbf{\mbox{intercept regression
of the line}}line}}
regression ~=~~=~
r \cdot \frac{\mbox{SD
\mbox{average of }yof~‑~
}y}{\mbox{SD
\mbox{slope}of }x}
\cdot\] \mbox{average of }x \]
The three functions below compute the correlation, slope, and intercept. All of them take three arguments: the name of the table, the label of the
column containing $x$, and the label of the column containing $y$.
def correlation(t, label_x, label_y):
return np.mean(standard_units(t.column(label_x))*standard_units(t.column(label_y)))

def slope(t, label_x, label_y):

r = correlation(t, label_x, label_y)
return r*np.std(t.column(label_y))/np.std(t.column(label_x))

def intercept(t, label_x, label_y):

return np.mean(t.column(label_y)) - slope(t, label_x,
label_y)*np.mean(t.column(label_x))

15.2.6. The Regression Line in the Units of the Data

The correlation between midparent height and child’s height is 0.32:
family_r = correlation(heights, 'MidParent', 'Child')
family_r

0.32094989606395924

We can also find the equation of the regression line for predicting the child’s height based on midparent height.
family_slope = slope(heights, 'MidParent', 'Child')
family_intercept = intercept(heights, 'MidParent', 'Child')
family_slope, family_intercept

(0.637360896969479, 22.63624054958975)

The equation of the regression line is

\[ \mbox{estimate of child's height} ~=~ 0.64 \cdot \mbox{midparent height} ~+~ 22.64 \]
This is also known as the regression equation. The principal use of the regression equation is to predict $y$ based on $x$.
For example, for a midparent height of 70.48 inches, the regression equation predicts the child’s height to be 67.56 inches.
family_slope * 70.48 + family_intercept

67.55743656799862

Our original prediction, created by taking the average height of all children who had midparent heights close to 70.48, came out to be pretty close:
67.63 inches compared to the regression line’s prediction of 67.55 inches.
heights_with_predictions.where('MidParent', are.equal_to(70.48)).show(3)

MidParent Child Prediction

70.48 74 67.6342
70.48 70 67.6342
70.48 68 67.6342
... (5 rows omitted)
Here are all of the rows of the table, along with our original predictions and the new regression predictions of the children’s heights.
heights_with_predictions = heights_with_predictions.with_column(
'Regression Prediction', family_slope * heights.column('MidParent') +
family_intercept
)
heights_with_predictions

MidParent Child Prediction Regression Prediction

75.43 73.2 70.1 70.7124
75.43 69.2 70.1 70.7124
75.43 69 70.1 70.7124
75.43 69 70.1 70.7124
73.66 73.5 70.4158 69.5842
73.66 72.5 70.4158 69.5842
73.66 65.5 70.4158 69.5842
73.66 65.5 70.4158 69.5842
72.06 71 68.5025 68.5645
72.06 68 68.5025 68.5645
... (924 rows omitted)
heights_with_predictions.scatter('MidParent')
The grey dots show the regression predictions, all on the regression line. Notice how the line is very close to the gold graph of averages. For these
data, the regression line does a good job of approximating the centers of the vertical strips.

15.2.7. Fitted Values

The predictions all lie on the line and are known as the “fitted values”. The function fit takes the name of the table and the labels of $x$ and $y$,
and returns an array of fitted values, one fitted value for each point in the scatter plot.
def fit(table, x, y):
"""Return the height of the regression line at each x value."""
a = slope(table, x, y)
b = intercept(table, x, y)
return a * table.column(x) + b

It is easier to see the line in the graph below than in the one above.
heights.with_column('Fitted', fit(heights, 'MidParent', 'Child')).scatter('MidParent')

Another way to draw the line is to use the option fit_line=True with the Table method scatter.
heights.scatter('MidParent', fit_line=True)
15.2.8. Units of Measurement of the Slope
The slope is a ratio, and it worth taking a moment to study the units in which it is measured. Our example comes from the familiar dataset about
mothers who gave birth in a hospital system. The scatter plot of pregnancy weights versus heights looks like a football that has been used in one
game too many, but it’s close enough to a football that we can justify putting our fitted line through it. In later sections we will see how to make such
justifications more formal.
baby = Table.read_table(path_data + 'baby.csv')

baby.scatter('Maternal Height', 'Maternal Pregnancy Weight', fit_line=True)

slope(baby, 'Maternal Height', 'Maternal Pregnancy Weight')

3.572846259275056

The slope of the regression line is 3.57 pounds per inch. This means that for two women who are 1 inch apart in height, our prediction of pregnancy
weight will differ by 3.57 pounds. For a woman who is 2 inches taller than another, our prediction of pregnancy weight will be
\[ 2 \times 3.57 ~=~ 7.14 \]
pounds more than our prediction for the shorter woman.
Notice that the successive vertical strips in the scatter plot are one inch apart, because the heights have been rounded to the nearest inch. Another
way to think about the slope is to take any two consecutive strips (which are necessarily 1 inch apart), corresponding to two groups of women who
are separated by 1 inch in height. The slope of 3.57 pounds per inch means that the average pregnancy weight of the taller group is about 3.57
pounds more than that of the shorter group.

15.2.9. Example
Suppose that our goal is to use regression to estimate the height of a basset hound based on its weight, using a sample that looks consistent with the
regression model. Suppose the observed correlation $r$ is 0.5, and that the summary statistics for the two variables are as in the table below:
average SD
height 14 inches 2 inches
weight 50 pounds 5 pounds
To calculate the equation of the regression line, we need the slope and the intercept.
\[ \mbox{slope} ~=~ \frac{r \cdot \mbox{SD of }y}{\mbox{SD of }x} ~=~ \frac{0.5 \cdot 2 \mbox{ inches}}{5 \mbox{ pounds}} ~=~ 0.2 ~\mbox{inches
per pound} \] ~=~ \mbox{average of }y ‑ \mbox{slope}\cdot \mbox{average of } x ~=~ 14 \mbox{ inches} ~‑~ 0.2 \mbox{ inches per pound} \cdot
\[ \mbox{intercept}
50 \mbox{ pounds} ~=~ 4 \mbox{ inches} \]
The equation of the regression line allows us to calculate the estimated height, in inches, based on a given weight in pounds:
\[ \mbox{estimated height} ~=~ 0.2 \cdot \mbox{given weight} ~+~ 4 \]
The slope of the line is measures the increase in the estimated height per unit increase in weight. The slope is positive, and it is important to note that
this does not mean that we think basset hounds get taller if they put on weight. The slope reflects the difference in the average heights of two groups
of dogs that are 1 pound apart in weight. Specifically, consider a group of dogs whose weight is $w$ pounds, and the group whose weight is $w+1$
pounds. The second group is estimated to be 0.2 inches taller, on average. This is true for all values of $w$ in the sample.
In general, the slope of the regression line can be interpreted as the average increase in $y$ per unit increase in $x$. Note that if the slope is
negative, then for every unit increase in $x$, the average of $y$ decreases.

15.2.10. Endnote
Even though we won’t establish the mathematical basis for the regression equation, we can see that it gives pretty good predictions when the scatter
plot is football shaped. It is a surprising mathematical fact that no matter what the shape of the scatter plot, the same equation gives the “best”
among all straight lines. That’s the topic of the next section.

15.3. The Method of Least Squares

We have developed the equation of the regression line that runs through a football shaped scatter plot. But not all scatter plots are football shaped,
not even linear ones. Does every scatter plot have a “best” line that goes through it? If so, can we still use the formulas for the slope and intercept
developed in the previous section, or do we need new ones?
To address these questions, we need a reasonable definition of “best”. Recall that the purpose of the line is to predict or estimate values of $y$,
given values of $x$. Estimates typically aren’t perfect. Each one is off the true value by an error. A reasonable criterion for a line to be the “best” is
for it to have the smallest possible overall error among all straight lines.
In this section we will make this criterion precise and see if we can identify the best straight line under the criterion.
Our first example is a dataset that has one row for every chapter of the novel “Little Women.” The goal is to estimate the number of characters (that
is, letters, spaces punctuation marks, and so on) based on the number of periods. Recall that we attempted to do this in the very first lecture of this
course.
little_women = Table.read_table(path_data + 'little_women.csv')
little_women = little_women.move_to_start('Periods')
little_women.show(3)

Periods Characters
189 21759
188 22148
231 20558
... (44 rows omitted)
little_women.scatter('Periods', 'Characters')
To explore the data, we will need to use the functions correlation, slope, intercept, and fit defined in the previous section.
correlation(little_women, 'Periods', 'Characters')

0.9229576895854816

The scatter plot is remarkably close to linear, and the correlation is more than 0.92.

15.3.1. Error in Estimation

The graph below shows the scatter plot and line that we developed in the previous section. We don’t yet know if that’s the best among all lines. We
first have to say precisely what “best” means.
lw_with_predictions = little_women.with_column('Linear Prediction', fit(little_women,
'Periods', 'Characters'))
lw_with_predictions.scatter('Periods')

Corresponding to each point on the scatter plot, there is an error of prediction calculated as the actual value minus the predicted value. It is the
vertical distance between the point and the line, with a negative sign if the point is below the line.
actual = lw_with_predictions.column('Characters')
predicted = lw_with_predictions.column('Linear Prediction')
errors = actual - predicted

lw_with_predictions.with_column('Error', errors)
Periods Characters Linear Prediction Error
189 21759 21183.6 575.403
188 22148 21096.6 1051.38
231 20558 24836.7 ‑4278.67
195 25526 21705.5 3820.54
255 23395 26924.1 ‑3529.13
140 14622 16921.7 ‑2299.68
131 14431 16138.9 ‑1707.88
214 22476 23358 ‑882.043
337 33767 34056.3 ‑289.317
185 18508 20835.7 ‑2327.69
... (37 rows omitted)
We can use slope and intercept to calculate the slope and intercept of the fitted line. The graph below shows the line (in light blue). The errors
corresponding to four of the points are shown in red. There is nothing special about those four points. They were just chosen for clarity of the display.
The function lw_errors takes a slope and an intercept (in that order) as its arguments and draws the figure.
lw_reg_slope = slope(little_women, 'Periods', 'Characters')
lw_reg_intercept = intercept(little_women, 'Periods', 'Characters')

print('Slope of Regression Line: ', np.round(lw_reg_slope), 'characters per period')

print('Intercept of Regression Line:', np.round(lw_reg_intercept), 'characters')
lw_errors(lw_reg_slope, lw_reg_intercept)

Slope of Regression Line: 87.0 characters per period

Intercept of Regression Line: 4745.0 characters

Had we used a different line to create our estimates, the errors would have been different. The graph below shows how big the errors would be if we
were to use another line for estimation. The second graph shows large errors obtained by using a line that is downright silly.
lw_errors(50, 10000)
lw_errors(-100, 50000)

15.3.2. Root Mean Squared Error

What we need now is one overall measure of the rough size of the errors. You will recognize the approach to creating this – it’s exactly the way we
developed the SD.
If you use any arbitrary line to calculate your estimates, then some of your errors are likely to be positive and others negative. To avoid cancellation
when measuring the rough size of the errors, we will take the mean of the squared errors rather than the mean of the errors themselves.
The mean squared error of estimation is a measure of roughly how big the squared errors are, but as we have noted earlier, its units are hard to
interpret. Taking the square root yields the root mean square error (rmse), which is in the same units as the variable being predicted and therefore
much easier to understand.

15.3.3. Minimizing the Root Mean Squared Error

Our observations so far can be summarized as follows.
To get estimates of $y$ based on $x$, you can use any line you want.
Every line has a root mean squared error of estimation.
“Better” lines have smaller errors.
Is there a “best” line? That is, is there a line that minimizes the root mean squared error among all lines?
To answer this question, we will start by defining a function lw_rmse to compute the root mean squared error of any line through the Little Women
scatter diagram. The function takes the slope and the intercept (in that order) as its arguments.
def lw_rmse(slope, intercept):
lw_errors(slope, intercept)
x = little_women.column('Periods')
y = little_women.column('Characters')
fitted = slope * x + intercept
mse = np.mean((y - fitted) ** 2)
print("Root mean squared error:", mse ** 0.5)

lw_rmse(50, 10000)

Root mean squared error: 4322.167831766537

lw_rmse(-100, 50000)

Root mean squared error: 16710.11983735375

Bad lines have big values of rmse, as expected. But the rmse is much smaller if we choose a slope and intercept close to those of the regression line.
lw_rmse(90, 4000)
Root mean squared error: 2715.5391063834586

Here is the root mean squared error corresponding to the regression line. By a remarkable fact of mathematics, no other line can beat this one.
The regression line is the unique straight line that minimizes the mean squared error of estimation among all straight lines.
lw_rmse(lw_reg_slope, lw_reg_intercept)

Root mean squared error: 2701.690785311856

The proof of this statement requires abstract mathematics that is beyond the scope of this course. On the other hand, we do have a powerful tool –
Python – that performs large numerical computations with ease. So we can use Python to confirm that the regression line minimizes the mean
squared error.

15.3.3.1. Numerical Optimization

First note that a line that minimizes the root mean squared error is also a line that minimizes the squared error. The square root makes no difference
to the minimization. So we will save ourselves a step of computation and just minimize the mean squared error (mse).
We are trying to predict the number of characters ($y$) based on the number of periods ($x$) in chapters of Little Women. If we use the line
\[ \mbox{prediction} ~=~ ax + b \]
it will have an mse that depends on the slope $a$ and the intercept $b$. The function lw_mse takes the slope and intercept as its arguments and
returns the corresponding mse.
def lw_mse(any_slope, any_intercept):
x = little_women.column('Periods')
y = little_women.column('Characters')
fitted = any_slope*x + any_intercept
return np.mean((y - fitted) ** 2)

Let’s check that lw_mse gets the right answer for the root mean squared error of the regression line. Remember that lw_mse returns the mean
squared error, so we have to take the square root to get the rmse.
lw_mse(lw_reg_slope, lw_reg_intercept)**0.5

2701.690785311856

That’s the same as the value we got by using lw_rmse earlier:

lw_rmse(lw_reg_slope, lw_reg_intercept)

Root mean squared error: 2701.690785311856

You can confirm that lw_mse returns the correct value for other slopes and intercepts too. For example, here is the rmse of the extremely bad line that
we tried earlier.
lw_mse(-100, 50000)**0.5

16710.11983735375

And here is the rmse for a line that is close to the regression line.
lw_mse(90, 4000)**0.5

2715.5391063834586

If we experiment with different values, we can find a low‑error slope and intercept through trial and error, but that would take a while. Fortunately,
there is a Python function that does all the trial and error for us.
The minimize function can be used to find the arguments of a function for which the function returns its minimum value. Python uses a similar trial‑
and‑error approach, following the changes that lead to incrementally lower output values.
The argument of minimize is a function that itself takes numerical arguments and returns a numerical value. For example, the function lw_mse takes a
numerical slope and intercept as its arguments and returns the corresponding mse.
The call minimize(lw_mse) returns an array consisting of the slope and the intercept that minimize the mse. These minimizing values are excellent
approximations arrived at by intelligent trial‑and‑error, not exact values based on formulas.
best = minimize(lw_mse)
best

array([ 86.97784117, 4744.78484535])

These values are the same as the values we calculated earlier by using the slope and intercept functions. We see small deviations due to the
inexact nature of minimize, but the values are essentially the same.
print("slope from formula: ", lw_reg_slope)
print("slope from minimize: ", best.item(0))
print("intercept from formula: ", lw_reg_intercept)
print("intercept from minimize: ", best.item(1))

slope from formula: 86.97784125829821

slope from minimize: 86.97784116615884
intercept from formula: 4744.784796574928
intercept from minimize: 4744.784845352655

15.3.4. The Least Squares Line

Therefore, we have found not only that the regression line minimizes mean squared error, but also that minimizing mean squared error gives us the
regression line. The regression line is the only line that minimizes mean squared error.
That is why the regression line is sometimes called the “least squares line.”

15.4. Least Squares Regression

In an earlier section, we developed formulas for the slope and intercept of the regression line through a football shaped scatter diagram. It turns out
that the slope and intercept of the least squares line have the same formulas as those we developed, regardless of the shape of the scatter plot.
We saw this in the example about Little Women, but let’s confirm it in an example where the scatter plot clearly isn’t football shaped. For the data, we
are once again indebted to the rich data archive of Prof. Larry Winner of the University of Florida. A 2013 study in the International Journal of Exercise
Science studied collegiate shot put athletes and examined the relation between strength and shot put distance. The population consists of 28 female
collegiate athletes. Strength was measured by the the biggest amount (in kilograms) that the athlete lifted in the “1RM power clean” in the pre‑
season. The distance (in meters) was the athlete’s personal best.
shotput = Table.read_table(path_data + 'shotput.csv')

shotput

Weight Lifted Shot Put Distance

37.5 6.4
51.5 10.2
61.3 12.4
61.3 13
63.6 13.2
66.1 13
70 12.7
92.7 13.9
90.5 15.5
90.5 15.8
... (18 rows omitted)
shotput.scatter('Weight Lifted')
That’s not a football shaped scatter plot. In fact, it seems to have a slight non‑linear component. But if we insist on using a straight line to make our
predictions, there is still one best straight line among all straight lines.
Our formulas for the slope and intercept of the regression line, derived for football shaped scatter plots, give the following values.
slope(shotput, 'Weight Lifted', 'Shot Put Distance')

0.09834382159781997

intercept(shotput, 'Weight Lifted', 'Shot Put Distance')

5.959629098373952

Does it still make sense to use these formulas even though the scatter plot isn’t football shaped? We can answer this by finding the slope and
intercept of the line that minimizes the mse.
We will define the function shotput_linear_mse to take an arbirtary slope and intercept as arguments and return the corresponding mse. Then
minimize applied to shotput_linear_mse will return the best slope and intercept.

def shotput_linear_mse(any_slope, any_intercept):

x = shotput.column('Weight Lifted')
y = shotput.column('Shot Put Distance')
fitted = any_slope*x + any_intercept
return np.mean((y - fitted) ** 2)

minimize(shotput_linear_mse)

array([0.09834382, 5.95962911])

These values are the same as those we got by using our formulas. To summarize:
No matter what the shape of the scatter plot, there is a unique line that minimizes the mean squared error of estimation. It is called the
regression line, and its slope and intercept are given by
\[\[ \mathbf{\mbox{slope of the
\mathbf{\mbox{intercept regression
of the line}}line}}
regression ~=~~=~
r \cdot \frac{\mbox{SD
\mbox{average of }yof~‑~
}y}{\mbox{SD
\mbox{slope}of }x}
\cdot\] \mbox{average of }x \]
fitted = fit(shotput, 'Weight Lifted', 'Shot Put Distance')
shotput.with_column('Best Straight Line', fitted).scatter('Weight Lifted')
15.4.1. Nonlinear Regression
The graph above reinforces our earlier observation that the scatter plot is a bit curved. So it is better to fit a curve than a straight line. The study
postulated a quadratic relation between the weight lifted and the shot put distance. So let’s use quadratic functions as our predictors and see if we
can find the best one.
We have to find the best quadratic function among all quadratic functions, instead of the best straight line among all straight lines. The method of
least squares allows us to do this.
The mathematics of this minimization is complicated and not easy to see just by examining the scatter plot. But numerical minimization is just as easy
as it was with linear predictors! We can get the best quadratic predictor by once again using minimize. Let’s see how this works.
Recall that a quadratic function has the form
\[ f(x) ~=~ ax^2 + bx + c \]
for constants $a$, $b$, and $c$.
To find the best quadratic function to predict distance based on weight lifted, using the criterion of least squares, we will first write a function that
takes the three constants as its arguments, calculates the fitted values by using the quadratic function above, and then returns the mean squared
error.
The function is called shotput_quadratic_mse. Notice that the definition is analogous to that of lw_mse, except that the fitted values are based on a
quadratic function instead of linear.
def shotput_quadratic_mse(a, b, c):
x = shotput.column('Weight Lifted')
y = shotput.column('Shot Put Distance')
fitted = a*(x**2) + b*x + c
return np.mean((y - fitted) ** 2)

We can now use minimize just as before to find the constants that minimize the mean squared error.
best = minimize(shotput_quadratic_mse)
best

array([-1.04004838e-03, 2.82708045e-01, -1.53182115e+00])

Our prediction of the shot put distance for an athlete who lifts $x$ kilograms is about
\[ ‑0.00104x^2 ~+~ 0.2827x ‑ 1.5318 \]
meters. For example, if the athlete can lift 100 kilograms, the predicted distance is 16.33 meters. On the scatter plot, that’s near the center of a
vertical strip around 100 kilograms.
(-0.00104)*(100**2) + 0.2827*100 - 1.5318

16.3382
Here are the predictions for all the values of Weight Lifted. You can see that they go through the center of the scatter plot, to a rough
approximation.
x = shotput.column(0)
shotput_fit = best.item(0)*(x**2) + best.item(1)*x + best.item(2)

shotput.with_column('Best Quadratic Curve', shotput_fit).scatter(0)

Note: We fit a quadratic here because it was suggested in the original study. But it is worth noting that at the rightmost end of the graph, the
quadratic curve appears to be close to peaking, after which the curve will start going downwards. So we might not want to use this model for new
athletes who can lift weights much higher than those in our data set.

15.5. Visual Diagnostics

Suppose a data scientist has decided to use linear regression to estimate values of one variable (called the response variable) based on another
variable (called the predictor). To see how well this method of estimation performs, the data scientist must measure how far off the estimates are
from the actual values. These differences are called residuals.
\[ \mbox{residual} ~=~ \mbox{observed value} ~‑~ \mbox{regression estimate} \]
A residual is what’s left over – the residue – after estimation.
Residuals are the vertical distances of the points from the regression line. There is one residual for each point in the scatter plot. The residual is the
difference between the observed value of $y$ and the fitted value of $y$, so for the point $(x, y)$,
\[ \mbox{residual} ~~ = ~~ y ~‑~ \mbox{fitted value of }y ~~ = ~~ y ~‑~ \mbox{height of regression line at }x \]
The function residual calculates the residuals. The calculation assumes all the relevant functions we have already defined: standard_units,
correlation, slope, intercept, and fit.

def residual(table, x, y):

return table.column(y) - fit(table, x, y)

Continuing our example of estimating the heights of adult children (the response) based on the midparent height (the predictor), let us calculate the
fitted values and the residuals.
heights = heights.with_columns(
'Fitted Value', fit(heights, 'MidParent', 'Child'),
'Residual', residual(heights, 'MidParent', 'Child')
)
heights
MidParent Child Fitted Value Residual
75.43 73.2 70.7124 2.48763
75.43 69.2 70.7124 ‑1.51237
75.43 69 70.7124 ‑1.71237
75.43 69 70.7124 ‑1.71237
73.66 73.5 69.5842 3.91576
73.66 72.5 69.5842 2.91576
73.66 65.5 69.5842 ‑4.08424
73.66 65.5 69.5842 ‑4.08424
72.06 71 68.5645 2.43553
72.06 68 68.5645 ‑0.564467
... (924 rows omitted)
When there are so many variables to work with, it is always helpful to start with visualization. The function scatter_fit draws the scatter plot of the
data, as well as the regression line.
def scatter_fit(table, x, y):
table.scatter(x, y, s=15)
plots.plot(table.column(x), fit(table, x, y), lw=4, color='gold')
plots.xlabel(x)
plots.ylabel(y)

scatter_fit(heights, 'MidParent', 'Child')

A residual plot can be drawn by plotting the residuals against the predictor variable. The function residual_plot does just that.
def residual_plot(table, x, y):
x_array = table.column(x)
t = Table().with_columns(
x, x_array,
'residuals', residual(table, x, y)
)
t.scatter(x, 'residuals', color='r')
xlims = make_array(min(x_array), max(x_array))
plots.plot(xlims, make_array(0, 0), color='darkblue', lw=4)
plots.title('Residual Plot')

residual_plot(heights, 'MidParent', 'Child')

The midparent heights are on the horizontal axis, as in the original scatter plot. But now the vertical axis shows the residuals. Notice that the plot
appears to be centered around the horizontal line at the level 0 (shown in dark blue). Notice also that the plot shows no upward or downward trend.
We will observe later that this lack of trend is true of all regressions.

15.5.1. Regression Diagnostics

Residual plots help us make visual assessments of the quality of a linear regression analysis. Such assessments are called diagnostics. The function
regression_diagnostic_plots draws the original scatter plot as well as the residual plot for ease of comparison.

def regression_diagnostic_plots(table, x, y):

scatter_fit(table, x, y)
residual_plot(table, x, y)

regression_diagnostic_plots(heights, 'MidParent', 'Child')

This residual plot indicates that linear regression was a reasonable method of estimation. Notice how the residuals are distributed fairly symmetrically
above and below the horizontal line at 0, corresponding to the original scatter plot being roughly symmetrical above and below. Notice also that the
vertical spread of the plot is fairly even across the most common values of the children’s heights. In other words, apart from a few outlying points, the
plot isn’t narrower in some places and wider in others.
In other words, the accuracy of the regression appears to be about the same across the observed range of the predictor variable.
The residual plot of a good regression shows no pattern. The residuals look about the same, above and below the horizontal line at 0, across
the range of the predictor variable.

15.5.2. Detecting Nonlinearity

Drawing the scatter plot of the data usually gives an indication of whether the relation between the two variables is non‑linear. Often, however, it is
easier to spot non‑linearity in a residual plot than in the original scatter plot. This is usually because of the scales of the two plots: the residual plot
allows us to zoom in on the errors and hence makes it easier to spot patterns.

Our data are a dataset on the age and length of dugongs, which are marine mammals related to manatees and sea cows (image from Wikimedia
Commons). The data are in a table called dugong. Age is measured in years and length in meters. Because dugongs tend not to keep track of their
birthdays, ages are estimated based on variables such as the condition of their teeth.
dugong = Table.read_table(path_data + 'dugongs.csv')
dugong = dugong.move_to_start('Length')
dugong

Length Age
1.8 1
1.85 1.5
1.87 1.5
1.77 1.5
2.02 2.5
2.27 4
2.15 5
2.26 5
2.35 7
2.47 8
... (17 rows omitted)
If we could measure the length of a dugong, what could we say about its age? Let’s examine what our data say. Here is a regression of age (the
response) on length (the predictor). The correlation between the two variables is substantial, at 0.83.
correlation(dugong, 'Length', 'Age')

0.8296474554905714

High correlation notwithstanding, the plot shows a curved pattern that is much more visible in the residual plot.
regression_diagnostic_plots(dugong, 'Length', 'Age')

While you can spot the non‑linearity in the original scatter, it is more clearly evident in the residual plot.
At the low end of the lengths, the residuals are almost all positive; then they are almost all negative; then positive again at the high end of lengths. In
other words the regression estimates have a pattern of being too high, then too low, then too high. That means it would have been better to use a
curve instead of a straight line to estimate the ages.
When a residual plot shows a pattern, there may be a non‑linear relation between the variables.

15.5.3. Detecting Heteroscedasticity

Heteroscedasticity is a word that will surely be of interest to those who are preparing for Spelling Bees. For data scientists, its interest lies in its
meaning, which is “uneven spread”.
Recall the table hybrid that contains data on hybrid cars in the U.S. Here is a regression of fuel efficiency on the rate of acceleration. The association
is negative: cars that accelearate quickly tend to be less efficient.
regression_diagnostic_plots(hybrid, 'acceleration', 'mpg')
Notice how the residual plot flares out towards the low end of the accelerations. In other words, the variability in the size of the errors is greater for
low values of acceleration than for high values. Uneven variation is often more easily noticed in a residual plot than in the original scatter plot.
If the residual plot shows uneven variation about the horizontal line at 0, the regression estimates are not equally accurate across the range
of the predictor variable.

15.6. Numerical Diagnostics

In addition to visualization, we can use numerical properties of residuals to assess the quality of regression. We will not prove these properties
mathematically. Rather, we will observe them by computation and see what they tell us about the regression.
All of the facts listed below hold for all shapes of scatter plots, whether or not they are linear.

15.6.1. Residual Plots Show No Trend

For every linear regression, whether good or bad, the residual plot shows no trend. Overall, it is flat. In other words, the residuals and the
predictor variable are uncorrelated.
You can see this in all the residual plots above. We can also calculate the correlation between the predictor variable and the residuals in each case.
correlation(heights, 'MidParent', 'Residual')

-2.719689807647064e-16

That doesn’t look like zero, but it is a tiny number that is 0 apart from rounding error due to computation. Here it is again, correct to 10 decimal
places. The minus sign is because of the rounding that above.
round(correlation(heights, 'MidParent', 'Residual'), 10)
-0.0

dugong = dugong.with_columns(
'Fitted Value', fit(dugong, 'Length', 'Age'),
'Residual', residual(dugong, 'Length', 'Age')
)
round(correlation(dugong, 'Length', 'Residual'), 10)

0.0

15.6.2. Average of Residuals

No matter what the shape of the scatter diagram, the average of the residuals is 0.
This is analogous to the fact that if you take any list of numbers and calculate the list of deviations from average, the average of the deviations is 0.
In all the residual plots above, you have seen the horizontal line at 0 going through the center of the plot. That is a visualization of this fact.
As a numerical example, here is the average of the residuals in the regression of children’s heights based on midparent heights.
round(np.mean(heights.column('Residual')), 10)

0.0

The same is true of the average of the residuals in the regression of the age of dugongs on their length. The mean of the residuals is 0, apart from
rounding error.
round(np.mean(dugong.column('Residual')), 10)

0.0

15.6.3. SD of the Residuals

No matter what the shape of the scatter plot, the SD of the residuals is a fraction of the SD of the response variable. The fraction is $\sqrt{1‑
r^2}$.
\[ \mbox{SD of residuals} ~=~ \sqrt{1 ‑ r^2} \cdot \mbox{SD of }y \]
We will soon see how this measures the accuracy of the regression estimate. But first, let’s confirm it by example.
In the case of children’s heights and midparent heights, the SD of the residuals is about 3.39 inches.
np.std(heights.column('Residual'))

3.3880799163953426

That’s the same as $\sqrt{1‑r^2}$ times the SD of response variable:

r = correlation(heights, 'MidParent', 'Child')
np.sqrt(1 - r**2) * np.std(heights.column('Child'))

3.388079916395342

The same is true for the regression of mileage on acceleration of hybrid cars. The correlation $r$ is negative (about ‑0.5), but $r^2$ is positive and
therefore $\sqrt{1‑r^2}$ is a fraction.
r = correlation(hybrid, 'acceleration', 'mpg')
r

-0.5060703843771186
hybrid = hybrid.with_columns(
'fitted mpg', fit(hybrid, 'acceleration', 'mpg'),
'residual', residual(hybrid, 'acceleration', 'mpg')
)
np.std(hybrid.column('residual')), np.sqrt(1 - r**2)*np.std(hybrid.column('mpg'))

(9.43273683343029, 9.43273683343029)

Now let us see how the SD of the residuals is a measure of how good the regression is. Remember that the average of the residuals is 0. Therefore
the smaller the SD of the residuals is, the closer the residuals are to 0. In other words, if the SD of the residuals is small, the overall size of the errors
in regression is small.
The extreme cases are when $r=1$ or $r=‑1$. In both cases, $\sqrt{1‑r^2} = 0$. Therefore the residuals have an average of 0 and an SD of 0 as well,
and therefore the residuals are all equal to 0. The regression line does a perfect job of estimation. As we saw earlier in this chapter, if $r = \pm 1$, the
scatter plot is a perfect straight line and is the same as the regression line, so indeed there is no error in the regression estimate.
But usually $r$ is not at the extremes. If $r$ is neither $\pm 1$ nor 0, then $\sqrt{1‑r^2}$ is a proper fraction, and the rough overall size of the error
of the regression estimate is somewhere between 0 and the SD of $y$.
The worst case is when $r = 0$. Then $\sqrt{1‑r^2} =1$, and the SD of the residuals is equal to the SD of $y$. This is consistent with the observation
that if $r=0$ then the regression line is a flat line at the average of $y$. In this situation, the root mean square error of regression is the root mean
squared deviation from the average of $y$, which is the SD of $y$. In practical terms, if $r = 0$ then there is no linear association between the two
variables, so there is no benefit in using linear regression.

15.6.4. Another Way to Interpret $r$

We can rewrite the result above to say that no matter what the shape of the scatter plot,
\[ \frac{\mbox{SD of residuals}}{\mbox{SD of }y} ~=~ \sqrt{1‑r^2} \]
A complementary result is that no matter what the shape of the scatter plot, the SD of the fitted values is a fraction of the SD of the observed values
of $y$. The fraction is $\vert r \vert$.
\[ \frac{\mbox{SD of fitted values}}{\mbox{SD of }y} ~=~ \vert r \vert \]
To see where the fraction comes in, notice that the fitted values are all on the regression line whereas the observed values of $y$ are the heights of
all the points in the scatter plot and are more variable.
scatter_fit(heights, 'MidParent', 'Child')

The fitted values range from about 64 to about 71, whereas the heights of all the children are quite a bit more variable, ranging from about 55 to 80.
To verify the result numerically, we just have to calculate both sides of the identity.
correlation(heights, 'MidParent', 'Child')

0.32094989606395924

Here is ratio of the SD of the fitted values and the SD of the observed values of birth weight:
np.std(heights.column('Fitted Value'))/np.std(heights.column('Child'))

0.32094989606395957

The ratio is equal to $r$, confirming our result.

Where does the absolute value come in? First note that as SDs can’t be negative, nor can a ratio of SDs. So what happens when $r$ is negative? The
example of fuel efficiency and acceleration will show us.
correlation(hybrid, 'acceleration', 'mpg')

-0.5060703843771186

np.std(hybrid.column('fitted mpg'))/np.std(hybrid.column('mpg'))

0.5060703843771186

The ratio of the two SDs is $\vert r \vert$.

A more standard way to express this result is to recall that
\[ \mbox{variance} ~=~ \mbox{mean squared deviation from average} ~=~ \mbox{SD}^2 \]
and therefore, by squaring both sides of our result,
\[ \frac{\mbox{variance of fitted values}}{\mbox{variance of }y} ~=~ r^2 \]

16. Inference for Regression

Thus far, our analysis of the relation between variables has been purely descriptive. We know how to find the best straight line to draw through a
scatter plot. The line is the best in the sense that it has the smallest mean squared error of estimation among all straight lines.
But what if our data were only a sample from a larger population? If in the sample we found a linear relation between the two variables, would the
same be true for the population? Would it be exactly the same linear relation? Could we predict the response of a new individual who is not in our
sample?
Such questions of inference and prediction arise if we believe that a scatter plot reflects the underlying relation between the two variables being
plotted but does not specify the relation completely. For example, a scatter plot of birth weight versus gestational days shows us the precise relation
between the two variables in our sample; but we might wonder whether that relation holds true, or almost true, for all babies in the population from
which the sample was drawn, or indeed among babies in general.
As always, inferential thinking begins with a careful examination of the assumptions about the data. Sets of assumptions are known as models. Sets
of assumptions about randomness in roughly linear scatter plots are called regression models.

16.1. A Regression Model

In brief, such models say that the underlying relation between the two variables is perfectly linear; this straight line is the signal that we would like to
identify. However, we are not able to see the line clearly. What we see are points that are scattered around the line. In each of the points, the signal
has been contaminated by random noise. Our inferential goal, therefore, is to separate the signal from the noise.
In greater detail, the regression model specifies that the points in the scatter plot are generated at random as follows.
The relation between $x$ and $y$ is perfectly linear. We cannot see this “true line” but it exists.
The scatter plot is created by taking points on the line and pushing them off the line vertically, either above or below, as follows:
For each $x$, find the corresponding point on the true line (that’s the signal), and then generate the noise or error.
The errors are drawn at random with replacement from a population of errors that has a normal distribution with mean 0.
Create a point whose horizontal coordinate is $x$ and whose vertical coordinate is “the height of the true line at $x$, plus the error”.
Finally, erase the true line from the scatter, and display just the points created.
Based on this scatter plot, how should we estimate the true line? The best line that we can put through a scatter plot is the regression line. So the
regression line is a natural estimate of the true line.
The simulation below shows how close the regression line is to the true line. The first panel shows how the scatter plot is generated from the true line.
The second shows the scatter plot that we see. The third shows the regression line through the plot. The fourth shows both the regression line and
the true line.
To run the simulation, call the function draw_and_compare with three arguments: the slope of the true line, the intercept of the true line, and the
sample size.
Run the simulation a few times, with different values for the slope and intercept of the true line, and varying sample sizes. Because all the points are
generated according to the model, you will see that the regression line is a good estimate of the true line if the sample size is moderately large.
# The true line,
# the points created,
# and our estimate of the true line.
# Arguments: true slope, true intercept, number of points

draw_and_compare(4, -5, 10)

In reality, of course, we will never see the true line. What the simulation shows that if the regression model looks plausible, and if we have a large
sample, then the regression line is a good approximation to the true line.
16.2. Inference for the True Slope
Our simulations show that if the regression model holds and the sample size is large, then the regression line is likely to be close to the true line. This
allows us to estimate the slope of the true line.
We will use our familiar sample of mothers and their newborn babies to develop a method of estimating the slope of the true line. First, let’s see if we
believe that the regression model is an appropriate set of assumptions for describing the relation between birth weight and the number of gestational
days.
scatter_fit(baby, 'Gestational Days', 'Birth Weight')

correlation(baby, 'Gestational Days', 'Birth Weight')

0.40754279338885108

By and large, the scatter looks fairly evenly distributed around the line, though there are some points that are scattered on the outskirts of the main
cloud. The correlation is 0.4 and the regression line has a positive slope.
Does this reflect the fact that the true line has a positive slope? To answer this question, let us see if we can estimate the true slope. We certainly
have one estimate of it: the slope of our regression line. That’s about 0.47 ounces per day.
slope(baby, 'Gestational Days', 'Birth Weight')

0.46655687694921522

But had the scatter plot come out differently, the regression line would have been different and might have had a different slope. How do we figure
out how different the slope might have been?
We need another sample of points, so that we can draw the regression line through the new scatter plot and find its slope. But from where will get
another sample?
You have guessed it – we will bootstrap our original sample. That will give us a bootstrapped scatter plot, through which we can draw a regression
line.

16.2.1. Bootstrapping the Scatter Plot

We can simulate new samples by random sampling with replacement from the original sample, as many times as the original sample size. Each of
these new samples will give us a scatter plot. We will call that a bootstrapped scatter plot, and for short, we will call the entire process bootstrapping
the scatter plot.
Here is the original scatter diagram from the sample, and four replications of the bootstrap resampling procedure. Notice how the resampled scatter
plots are in general a little more sparse than the original. That is because some of the original points do not get selected in the samples.
16.2.2. Estimating the True Slope
We can bootstrap the scatter plot a large number of times, and draw a regression line through each bootstrapped plot. Each of those lines has a
slope. We can simply collect all the slopes and draw their empirical histogram. Recall that by default, the sample method draws at random with
replacement, the same number of times as the number of rows in the table. That is, sample generates a bootstrap sample by default.
slopes = make_array()
for i in np.arange(5000):
bootstrap_sample = baby.sample()
bootstrap_slope = slope(bootstrap_sample, 'Gestational Days', 'Birth Weight')
slopes = np.append(slopes, bootstrap_slope)
Table().with_column('Bootstrap Slopes', slopes).hist(bins=20)
We can then construct an approximate 95% confidence interval for the slope of the true line, using the bootstrap percentile method. The confidence
interval extends from the 2.5th percentile to the 97.5th percentile of the 5000 bootstrapped slopes.
left = percentile(2.5, slopes)
right = percentile(97.5, slopes)
left, right

(0.38169251837495338, 0.55839374914417184)

An approximate 95% confidence interval for the true slope extends from about 0.38 ounces per day to about 0.56 ounces per day.

16.2.3. A Function to Bootstrap the Slope

Let us collect all the steps of our method of estimating the slope and define a function bootstrap_slope that carries them out. Its arguments are the
name of the table and the labels of the predictor and response variables, and the desired number of bootstrap replications. In each replication, the
function bootstraps the original scatter plot and calculates the slope of the resulting regression line. It then draws the histogram of all the generated
slopes and prints the interval consisting of the “middle 95%” of the slopes.
def bootstrap_slope(table, x, y, repetitions):

# For each repetition:

# Bootstrap the scatter, get the slope of the regression line,
# augment the list of generated slopes
slopes = make_array()
for i in np.arange(repetitions):
bootstrap_sample = table.sample()
bootstrap_slope = slope(bootstrap_sample, x, y)
slopes = np.append(slopes, bootstrap_slope)

# Find the endpoints of the 95% confidence interval for the true slope
left = percentile(2.5, slopes)
right = percentile(97.5, slopes)

# Slope of the regression line from the original sample

observed_slope = slope(table, x, y)

# Display results
Table().with_column('Bootstrap Slopes', slopes).hist(bins=20)
plots.plot(make_array(left, right), make_array(0, 0), color='yellow', lw=8);
print('Slope of regression line:', observed_slope)
print('Approximate 95%-confidence interval for the true slope:')
print(left, right)

When we call bootstrap_slope to find a confidence interval for the true slope when the response variable is birth weight and the predictor is
gestational days, we get an interval very close to the one we obtained earlier: approximately 0.38 ounces per day to 0.56 ounces per day.
bootstrap_slope(baby, 'Gestational Days', 'Birth Weight', 5000)
Slope of regression line: 0.466556876949
Approximate 95%-confidence interval for the true slope:
0.380373502308 0.558711930778

Now that we have a function that automates our process of estimating the slope of the true line in a regression model, we can use it on other
variables as well.
For example, let’s examine the relation between birth weight and the mother’s height. Do taller women tend to have heavier babies?
The regression model seems reasonable, based on the scatter plot, but the correlation is not high. It’s just about 0.2.
scatter_fit(baby, 'Maternal Height', 'Birth Weight')

correlation(baby, 'Maternal Height', 'Birth Weight')

0.20370417718968034

As before, we can use bootstrap_slope to estimate the slope of the true line in the regression model.
bootstrap_slope(baby, 'Maternal Height', 'Birth Weight', 5000)

Slope of regression line: 1.47801935193

Approximate 95%-confidence interval for the true slope:
1.06617289982 1.91237018475
A 95% confidence interval for the true slope extends from about 1 ounce per inch to about 1.9 ounces per inch.

16.2.4. Could the True Slope Be 0?

Suppose we believe that our data follow the regression model, and we fit the regression line to estimate the true line. If the regression line isn’t
perfectly flat, as is almost invariably the case, we will be observing some linear association in the scatter plot.
But what if that observation is spurious? In other words, what if the true line was flat – that is, there was no linear relation between the two variables –
and the association that we observed was just due to randomness in generating the points that form our sample?
Here is a simulation that illustrates why this question arises. We will once again call the function draw_and_compare, this time requiring the true line to
have slope 0. Our goal is to see whether our regression line shows a slope that is not 0.
Remember that the arguments to the function draw_and_compare are the slope and the intercept of the true line, and the number of points to be
generated.
draw_and_compare(0, 10, 25)
Run the simulation a few times, keeping the slope of the true line 0 each time. You will notice that while the slope of the true line is 0, the slope of the
regression line is typically not 0. The regression line sometimes slopes upwards, and sometimes downwards, each time giving us a false impression
that the two variables are correlated.
To decide whether or not the slope that we are seeing is real, we would like to test the following hypotheses:
Null Hypothesis. The slope of the true line is 0.
Alternative Hypothesis. The slope of the true line is not 0.
We are well positioned to do this. Since we can construct a 95% confidence interval for the true slope, all we have to do is see whether the interval
contains 0.
If it doesn’t, then we can reject the null hypothesis (with the 5% cutoff for the P‑value).
If the confidence interval for the true slope does contain 0, then we don’t have enough evidence to reject the null hypothesis. Perhaps the slope that
we are seeing is spurious.
Let’s use this method in an example. Suppose we try to estimate the birth weight of the baby based on the mother’s age. Based on the sample, the
slope of the regression line for estimating birth weight based on maternal age is positive, about 0.08 ounces per year.
slope(baby, 'Maternal Age', 'Birth Weight')

0.085007669415825132

Though the slope is positive, it’s pretty small. The regression line is so close to flat that it raises the question of whether the true line is flat.
scatter_fit(baby, 'Maternal Age', 'Birth Weight')

We can use bootstrap_slope to estimate the slope of the true line. The calculation shows that an approximate 95% bootstrap confidence interval for
the true slope has a negative left end point and a positive right end point – in other words, the interval contains 0.
bootstrap_slope(baby, 'Maternal Age', 'Birth Weight', 5000)

Slope of regression line: 0.0850076694158

Approximate 95%-confidence interval for the true slope:
-0.104436940365 0.276512953946
Because the interval contains 0, we cannot reject the null hypothesis that the slope of the true linear relation between maternal age and baby’s birth
weight is 0. Based on this analysis, it would be unwise to predict birth weight based on the regression model with maternal age as the predictor.

16.3. Prediction Intervals

One of the primary uses of regression is to make predictions for a new individual who was not part of our original sample but is similar to the sampled
individuals. In the language of the model, we want to estimate $y$ for a new value of $x$.
Our estimate is the height of the true line at $x$. Of course, we don’t know the true line. What we have as a substitute is the regression line through
our sample of points.
The fitted value at a given value of $x$ is the regression estimate of $y$ based on that value of $x$. In other words, the fitted value at a given value
of $x$ is the height of the regression line at that $x$.
Suppose we try to predict a baby’s birth weight based on the number of gestational days. As we saw in the previous section, the data fit the
regression model fairly well and a 95% confidence interval for the slope of the true line doesn’t contain 0. So it seems reasonable to carry out our
prediction.
The figure below shows where the prediction lies on the regression line. The red line is at $x = 300$.

The height of the point where the red line hits the regression line is the fitted value at 300 gestational days.
The function fitted_value computes this height. Like the functions correlation, slope, and intercept, its arguments include the name of the table
and the labels of the $x$ and $y$ columns. But it also requires a fourth argument, which is the value of $x$ at which the estimate will be made.
def fitted_value(table, x, y, given_x):
a = slope(table, x, y)
b = intercept(table, x, y)
return a * given_x + b

The fitted value at 300 gestational days is about 129.2 ounces. In other words, for a pregnancy that has a duration of 300 gestational days, our
estimate for the baby’s weight is about 129.2 ounces.
fit_300 = fitted_value(baby, 'Gestational Days', 'Birth Weight', 300)
fit_300

129.2129241703143

16.3.1. The Variability of the Prediction

We have developed a method making one prediction of a new baby’s birth weight based on the number of gestational days, using the data in our
sample. But as data scientists, we know that the sample might have been different. Had the sample been different, the regression line would have
been different too, and so would our prediction. To see how good our prediction is, we must get a sense of how variable the prediction can be.
To do this, we must generate new samples. We can do that by bootstrapping the scatter plot as in the previous section. We will then fit the regression
line to the scatter plot in each replication, and make a prediction based on each line. The figure below shows 10 such lines, and the corresponding
predicted birth weight at 300 gestational days.
The predictions vary from one line to the next. The table below shows the slope and intercept of each of the 10 lines, along with the prediction.
lines

slope intercept prediction at x=300

0.431704 ‑1.10973 128.402
0.512942 ‑23.6503 130.232
0.450939 ‑6.73161 128.55
0.447632 ‑5.68583 128.604
0.353555 20.1531 126.22
0.469301 ‑11.6276 129.163
0.445023 ‑5.01298 128.494
0.540571 ‑31.3711 130.8
0.487377 ‑16.8051 129.408
0.451658 ‑5.45954 130.038

16.3.2. Bootstrap Prediction Interval

If we increase the number of repetitions of the resampling process, we can generate an empirical histogram of the predictions. This will allow us to
create an interval of predictions, using the same percentile method that we used create a bootstrap confidence interval for the slope.
Let us define a function called bootstrap_prediction to do this. The function takes five arguments:
the name of the table
the column labels of the predictor and response variables, in that order
the value of $x$ at which to make the prediction
the desired number of bootstrap repetitions
In each repetition, the function bootstraps the original scatter plot and finds the predicted value of $y$ based on the specified value of $x$.
Specifically, it calls the function fitted_value that we defined earlier in this section to find the fitted value at the specified $x$.
Finally, it draws the empirical histogram of all the predicted values, and prints the interval consisting of the “middle 95%” of the predicted values. It
also prints the predicted value based on the regression line through the original scatter plot.
# Bootstrap prediction of variable y at new_x
# Data contained in table; prediction by regression of y based on x
# repetitions = number of bootstrap replications of the original scatter plot

def bootstrap_prediction(table, x, y, new_x, repetitions):

# For each repetition:

# Bootstrap the scatter;
# get the regression prediction at new_x;
# augment the predictions list
predictions = make_array()
for i in np.arange(repetitions):
bootstrap_sample = table.sample()
bootstrap_prediction = fitted_value(bootstrap_sample, x, y, new_x)
predictions = np.append(predictions, bootstrap_prediction)

# Find the ends of the approximate 95% prediction interval

left = percentile(2.5, predictions)
right = percentile(97.5, predictions)

# Prediction based on original sample

original = fitted_value(table, x, y, new_x)

# Display results
Table().with_column('Prediction', predictions).hist(bins=20)
plots.xlabel('predictions at x='+str(new_x))
plots.plot(make_array(left, right), make_array(0, 0), color='yellow', lw=8);
print('Height of regression line at x='+str(new_x)+':', original)
print('Approximate 95%-confidence interval:')
print(left, right)

bootstrap_prediction(baby, 'Gestational Days', 'Birth Weight', 300, 5000)

Height of regression line at x=300: 129.2129241703143

Approximate 95%-confidence interval:
127.30986480617071 131.3039886526053

The figure above shows a bootstrap empirical histogram of the predicted birth weight of a baby at 300 gestational days, based on 5,000 repetitions
of the bootstrap process. The empirical distribution is roughly normal.
An approximate 95% prediction interval of scores has been constructed by taking the “middle 95%” of the predictions, that is, the interval from the
2.5th percentile to the 97.5th percentile of the predictions. The interval ranges from about 127 to about 131. The prediction based on the original
sample was about 129, which is close to the center of the interval.

16.3.3. The Effect of Changing the Value of the Predictor

The figure below shows the histogram of 5,000 bootstrap predictions at 285 gestational days. The prediction based on the original sample is about
122 ounces, and the interval ranges from about 121 ounces to about 123 ounces.
bootstrap_prediction(baby, 'Gestational Days', 'Birth Weight', 285, 5000)
Height of regression line at x=285: 122.21457101607608
Approximate 95%-confidence interval:
121.15559627774567 123.29019769886106

Notice that this interval is narrower than the prediction interval at 300 gestational days. Let us investigate the reason for this.
The mean number of gestational days is about 279 days:
np.mean(baby.column('Gestational Days'))

279.1013628620102

So 285 is nearer to the center of the distribution than 300 is. Typically, the regression lines based on the bootstrap samples are closer to each other
near the center of the distribution of the predictor variable. Therefore all of the predicted values are closer together as well. This explains the
narrower width of the prediction interval.
You can see this in the figure below, which shows predictions at $x = 285$ and $x = 300$ for each of ten bootstrap replications. Typically, the lines
are farther apart at $x = 300$ than at $x = 285$, and therefore the predictions at $x = 300$ are more variable.

16.3.3.1. Words of caution

All of the predictions and tests that we have performed in this chapter assume that the regression model holds. Specifically, the methods assume
that the scatter plot resembles points generated by starting with points that are on a straight line and then pushing them off the line by adding
random normal noise.
If the scatter plot does not look like that, then perhaps the model does not hold for the data. If the model does not hold, then calculations that
assume the model to be true are not valid.
Therefore, we must first decide whether the regression model holds for our data, before we start making predictions based on the model or testing
hypotheses about parameters of the model. A simple way is to do what we did in this section, which is to draw the scatter diagram of the two
variables and see whether it looks roughly linear and evenly spread out around a line. We should also run the diagnostics we developed in the
previous section using the residual plot.

17. Classification
David Wagner is the primary author of this chapter.
Machine learning is a class of techniques for automatically finding patterns in data and using it to draw inferences or make predictions. You have
already seen linear regression, which is one kind of machine learning. This chapter introduces a new one: classification.
Classification is about learning how to make predictions from past examples. We are given some examples where we have been told what the correct
prediction was, and we want to learn from those examples how to make good predictions in the future. Here are a few applications where
classification is used in practice:
For each order Amazon receives, Amazon would like to predict: is this order fraudulent? They have some information about each order (e.g.,
its total value, whether the order is being shipped to an address this customer has used before, whether the shipping address is the same as
the credit card holder’s billing address). They have lots of data on past orders, and they know which of those past orders were fraudulent and
which weren’t. They want to learn patterns that will help them predict, as new orders arrive, whether those new orders are fraudulent.
Online dating sites would like to predict: are these two people compatible? Will they hit it off? They have lots of data on which matches
they’ve suggested to their customers in the past, and they have some idea which ones were successful. As new customers sign up, they’d like
to make predictions about who might be a good match for them.
Doctors would like to know: does this patient have cancer? Based on the measurements from some lab test, they’d like to be able to predict
whether the particular patient has cancer. They have lots of data on past patients, including their lab measurements and whether they ultimately
developed cancer, and from that, they’d like to try to infer what measurements tend to be characteristic of cancer (or non‑cancer) so they can
diagnose future patients accurately.
Politicians would like to predict: are you going to vote for them? This will help them focus fundraising efforts on people who are likely to
support them, and focus get‑out‑the‑vote efforts on voters who will vote for them. Public databases and commercial databases have a lot of
information about most people: e.g., whether they own a home or rent; whether they live in a rich neighborhood or poor neighborhood; their
interests and hobbies; their shopping habits; and so on. And political campaigns have surveyed some voters and found out who they plan to
vote for, so they have some examples where the correct answer is known. From this data, the campaigns would like to find patterns that will
help them make predictions about all other potential voters.
All of these are classification tasks. Notice that in each of these examples, the prediction is a yes/no question – we call this binary classification,
because there are only two possible predictions.
In a classification task, each individual or situation where we’d like to make a prediction is called an observation. We ordinarily have many
observations. Each observation has multiple attributes, which are known (for example, the total value of the order on Amazon, or the voter’s annual
salary). Also, each observation has a class, which is the answer to the question we care about (for example, fraudulent or not, or voting for you or
not).
When Amazon is predicting whether orders are fraudulent, each order corresponds to a single observation. Each observation has several attributes:
the total value of the order, whether the order is being shipped to an address this customer has used before, and so on. The class of the observation
is either 0 or 1, where 0 means that the order is not fraudulent and 1 means that the order is fraudulent. When a customer makes a new order, we do
not observe whether it is fraudulent, but we do observe its attributes, and we will try to predict its class using those attributes.
Classification requires data. It involves looking for patterns, and to find patterns, you need data. That’s where the data science comes in. In particular,
we’re going to assume that we have access to training data: a bunch of observations, where we know the class of each observation. The collection of
these pre‑classified observations is also called a training set. A classification algorithm is going to analyze the training set, and then come up with a
classifier: an algorithm for predicting the class of future observations.
Classifiers do not need to be perfect to be useful. They can be useful even if their accuracy is less than 100%. For instance, if the online dating site
occasionally makes a bad recommendation, that’s OK; their customers already expect to have to meet many people before they’ll find someone they
hit it off with. Of course, you don’t want the classifier to make too many errors — but it doesn’t have to get the right answer every single time.

17.1. Nearest Neighbors

In this section we’ll develop the nearest neighbor method of classification. Just focus on the ideas for now and don’t worry if some of the code is
mysterious. Later in the chapter we’ll see how to organize our ideas into code that performs the classification.

17.1.1. Chronic kidney disease

Let’s work through an example. We’re going to work with a data set that was collected to help doctors diagnose chronic kidney disease (CKD). Each
row in the data set represents a single patient who was treated in the past and whose diagnosis is known. For each patient, we have a bunch of
measurements from a blood test. We’d like to find which measurements are most useful for diagnosing CKD, and develop a way to classify future
patients as “has CKD” or “doesn’t have CKD” based on their blood test results.
ckd = Table.read_table(path_data + 'ckd.csv').relabeled('Blood Glucose Random',
'Glucose')
ckd

Blood Specific Albumin Sugar Red Pus Cell Bacteria

Age Pressure Gravity Blood Pus Cell clumps
Cells
48 70 1.005 4 0 normal abnormal present notpresent
53 90 1.02 2 0 abnormal abnormal present notpresent
63 70 1.01 3 0 abnormal abnormal present notpresent
68 80 1.01 3 2 normal abnormal present present
61 80 1.015 2 0 abnormal abnormal notpresent notpresent
48 80 1.025 4 0 normal abnormal notpresent notpresent
69 70 1.01 3 4 normal abnormal notpresent notpresent
73 70 1.005 0 0 normal normal notpresent notpresent
73 80 1.02 2 0 abnormal abnormal notpresent notpresent
46 60 1.01 1 0 normal normal notpresent notpresent
... (148 rows omitted)
Some of the variables are categorical (words like “abnormal”), and some quantitative. The quantitative variables all have different scales. We’re going
to want to make comparisons and estimate distances, often by eye, so let’s select just a few of the variables and work in standard units. Then we
won’t have to worry about the scale of each of the different variables.
ckd = Table().with_columns(
'Hemoglobin', standard_units(ckd.column('Hemoglobin')),
'Glucose', standard_units(ckd.column('Glucose')),
'White Blood Cell Count', standard_units(ckd.column('White Blood Cell Count')),
'Class', ckd.column('Class')
)

ckd

Hemoglobin Glucose White Blood Cell Count Class

‑0.865744 ‑0.221549 ‑0.569768 1
‑1.45745 ‑0.947597 1.16268 1
‑1.00497 3.84123 ‑1.27558 1
‑2.81488 0.396364 0.809777 1
‑2.08395 0.643529 0.232293 1
‑1.35303 ‑0.561402 ‑0.505603 1
‑0.413266 2.04928 0.360623 1
‑1.28342 ‑0.947597 3.34429 1
‑1.10939 1.87936 ‑0.409356 1
‑1.35303 0.489051 1.96475 1
... (148 rows omitted)
Let’s look at two columns in particular: the hemoglobin level (in the patient’s blood), and the blood glucose level (at a random time in the day; without
fasting specially for the blood test).
We’ll draw a scatter plot to visualize the relation between the two variables. Blue dots are patients with CKD; gold dots are patients without CKD.
What kind of medical test results seem to indicate CKD?
color_table = Table().with_columns(
'Class', make_array(1, 0),
'Color', make_array('darkblue', 'gold')
)
ckd = ckd.join('Class', color_table)

ckd.scatter('Hemoglobin', 'Glucose', group='Color')

Suppose Alice is a new patient who is not in the data set. If I tell you Alice’s hemoglobin level and blood glucose level, could you predict whether she
has CKD? It sure looks like it! You can see a very clear pattern here: points in the lower‑right tend to represent people who don’t have CKD, and the
rest tend to be folks with CKD. To a human, the pattern is obvious. But how can we program a computer to automatically detect patterns such as this
one?

17.1.2. A Nearest Neighbor Classifier

There are lots of kinds of patterns one might look for, and lots of algorithms for classification. But I’m going to tell you about one that turns out to be
surprisingly effective. It is called nearest neighbor classification. Here’s the idea. If we have Alice’s hemoglobin and glucose numbers, we can put her
somewhere on this scatterplot; the hemoglobin is her x‑coordinate, and the glucose is her y‑coordinate. Now, to predict whether she has CKD or not,
we find the nearest point in the scatterplot and check whether it is blue or gold; we predict that Alice should receive the same diagnosis as that
patient.
In other words, to classify Alice as CKD or not, we find the patient in the training set who is “nearest” to Alice, and then use that patient’s diagnosis as
our prediction for Alice. The intuition is that if two points are near each other in the scatterplot, then the corresponding measurements are pretty
similar, so we might expect them to receive the same diagnosis (more likely than not). We don’t know Alice’s diagnosis, but we do know the diagnosis
of all the patients in the training set, so we find the patient in the training set who is most similar to Alice, and use that patient’s diagnosis to predict
Alice’s diagnosis.
In the graph below, the red dot represents Alice. It is joined with a black line to the point that is nearest to it – its nearest neighbor in the training set.
The figure is drawn by a function called show_closest. It takes an array that represents the $x$ and $y$ coordinates of Alice’s point. Vary those to
see how the closest point changes! Note especially when the closest point is blue and when it is gold.
# In this example, Alice's Hemoglobin attribute is 0 and her Glucose is 1.5.
alice = make_array(0, 1.5)
show_closest(alice)
Thus our nearest neighbor classifier works like this:
Find the point in the training set that is nearest to the new point.
If that nearest point is a “CKD” point, classify the new point as “CKD”. If the nearest point is a “not CKD” point, classify the new point as “not
CKD”.
The scatterplot suggests that this nearest neighbor classifier should be pretty accurate. Points in the lower‑right will tend to receive a “no CKD”
diagnosis, as their nearest neighbor will be a gold point. The rest of the points will tend to receive a “CKD” diagnosis, as their nearest neighbor will be
a blue point. So the nearest neighbor strategy seems to capture our intuition pretty well, for this example.

17.1.3. Decision boundary

Sometimes a helpful way to visualize a classifier is to map out the kinds of attributes where the classifier would predict ‘CKD’, and the kinds where it
would predict ‘not CKD’. We end up with some boundary between the two, where points on one side of the boundary will be classified ‘CKD’ and
points on the other side will be classified ‘not CKD’. This boundary is called the decision boundary. Each different classifier will have a different
decision boundary; the decision boundary is just a way to visualize what criteria the classifier is using to classify points.
For example, suppose the coordinates of Alice’s point are (0, 1.5). Notice that the nearest neighbor is blue. Now try reducing the height (the $y$‑
coordinate) of the point. You’ll see that at around $y = 0.95$ the nearest neighbor turns from blue to gold.
alice = make_array(0, 0.97)
show_closest(alice)

Here are hundreds of new unclassified points, all in red.

Each of the red points has a nearest neighbor in the training set (the same blue and gold points as before). For some red points you can easily tell
whether the nearest neighbor is blue or gold. For others, it’s a little more tricky to make the decision by eye. Those are the points near the decision
boundary.
But the computer can easily determine the nearest neighbor of each point. So let’s get it to apply our nearest neighbor classifier to each of the red
points:
For each red point, it must find the closest point in the training set; it must then change the color of the red point to become the color of the nearest
neighbor.
The resulting graph shows which points will get classified as ‘CKD’ (all the blue ones), and which as ‘not CKD’ (all the gold ones).

The decision boundary is where the classifier switches from turning the red points blue to turning them gold.

17.1.4. k‑Nearest Neighbors

However, the separation between the two classes won’t always be quite so clean. For instance, suppose that instead of hemoglobin levels we were to
look at white blood cell count. Look at what happens:
ckd.scatter('White Blood Cell Count', 'Glucose', group='Color')
As you can see, non‑CKD individuals are all clustered in the lower‑left. Most of the patients with CKD are above or to the right of that cluster… but not
all. There are some patients with CKD who are in the lower left of the above figure (as indicated by the handful of blue dots scattered among the gold
cluster). What this means is that you can’t tell for certain whether someone has CKD from just these two blood test measurements.
If we are given Alice’s glucose level and white blood cell count, can we predict whether she has CKD? Yes, we can make a prediction, but we
shouldn’t expect it to be 100% accurate. Intuitively, it seems like there’s a natural strategy for predicting: plot where Alice lands in the scatter plot; if
she is in the lower‑left, predict that she doesn’t have CKD, otherwise predict she has CKD.
This isn’t perfect – our predictions will sometimes be wrong. (Take a minute and think it through: for which patients will it make a mistake?) As the
scatterplot above indicates, sometimes people with CKD have glucose and white blood cell levels that look identical to those of someone without
CKD, so any classifier is inevitably going to make the wrong prediction for them.
Can we automate this on a computer? Well, the nearest neighbor classifier would be a reasonable choice here too. Take a minute and think it through:
how will its predictions compare to those from the intuitive strategy above? When will they differ?
Its predictions will be pretty similar to our intuitive strategy, but occasionally it will make a different prediction. In particular, if Alice’s blood test results
happen to put her right near one of the blue dots in the lower‑left, the intuitive strategy would predict ‘not CKD’, whereas the nearest neighbor
classifier will predict ‘CKD’.
There is a simple generalization of the nearest neighbor classifier that fixes this anomaly. It is called the k‑nearest neighbor classifier. To predict
Alice’s diagnosis, rather than looking at just the one neighbor closest to her, we can look at the 3 points that are closest to her, and use the diagnosis
for each of those 3 points to predict Alice’s diagnosis. In particular, we’ll use the majority value among those 3 diagnoses as our prediction for Alice’s
diagnosis. Of course, there’s nothing special about the number 3: we could use 4, or 5, or more. (It’s often convenient to pick an odd number, so that
we don’t have to deal with ties.) In general, we pick a number $k$, and our predicted diagnosis for Alice is based on the $k$ patients in the training
set who are closest to Alice. Intuitively, these are the $k$ patients whose blood test results were most similar to Alice, so it seems reasonable to use
their diagnoses to predict Alice’s diagnosis.
The $k$‑nearest neighbor classifier will now behave just like our intuitive strategy above.

17.2. Training and Testing

How good is our nearest neighbor classifier? To answer this we’ll need to find out how frequently our classifications are correct. If a patient has
chronic kidney disease, how likely is our classifier to pick that up?
If the patient is in our training set, we can find out immediately. We already know what class the patient is in. So we can just compare our prediction
and the patient’s true class.
But the point of the classifier is to make predictions for new patients not in our training set. We don’t know what class these patients are in but we
can make a prediction based on our classifier. How to find out whether the prediction is correct?
One way is to wait for further medical tests on the patient and then check whether or not our prediction agrees with the test results. With that
approach, by the time we can say how likely our prediction is to be accurate, it is no longer useful for helping the patient.
Instead, we will try our classifier on some patients whose true classes are known. Then, we will compute the proportion of the time our classifier was
correct. This proportion will serve as an estimate of the proportion of all new patients whose class our classifier will accurately predict. This is called
testing.
17.2.1. Overly Optimistic “Testing”
The training set offers a very tempting set of patients on whom to test out our classifier, because we know the class of each patient in the training
set.
But let’s be careful … there will be pitfalls ahead if we take this path. An example will show us why.
Suppose we use a 1‑nearest neighbor classifier to predict whether a patient has chronic kidney disease, based on glucose and white blood cell count.
ckd.scatter('White Blood Cell Count', 'Glucose', group='Color')

Earlier, we said that we expect to get some classifications wrong, because there’s some intermingling of blue and gold points in the lower‑left.
But what about the points in the training set, that is, the points already on the scatter? Will we ever mis‑classify them?
The answer is no. Remember that 1‑nearest neighbor classification looks for the point in the training set that is nearest to the point being classified.
Well, if the point being classified is already in the training set, then its nearest neighbor in the training set is itself! And therefore it will be classified as
its own color, which will be correct because each point in the training set is already correctly colored.
In other words, if we use our training set to “test” our 1‑nearest neighbor classifier, the classifier will pass the test 100% of the time.
Mission accomplished. What a great classifier!
No, not so much. A new point in the lower‑left might easily be mis‑classified, as we noted earlier. “100% accuracy” was a nice dream while it lasted.
The lesson of this example is not to use the training set to test a classifier that is based on it.

17.2.2. Generating a Test Set

In earlier chapters, we saw that random sampling could be used to estimate the proportion of individuals in a population that met some criterion.
Unfortunately, we have just seen that the training set is not like a random sample from the population of all patients, in one important respect: Our
classifier guesses correctly for a higher proportion of individuals in the training set than it does for individuals in the population.
When we computed confidence intervals for numerical parameters, we wanted to have many new random samples from a population, but we only had
access to a single sample. We solved that problem by taking bootstrap resamples from our sample.
We will use an analogous idea to test our classifier. We will create two samples out of the original training set, use one of the samples as our training
set, and the other one for testing.
So we will have three groups of individuals:
a training set on which we can do any amount of exploration to build our classifier;
a separate testing set on which to try out our classifier and see what fraction of times it classifies correctly;
the underlying population of individuals for whom we don’t know the true classes; the hope is that our classifier will succeed about as well for
these individuals as it did for our testing set.
How to generate the training and testing sets? You’ve guessed it – we’ll select at random.
There are 158 individuals in ckd. Let’s use a random half of them for training and the other half for testing. To do this, we’ll shuffle all the rows, take
the first 79 as the training set, and the remaining 79 for testing.
shuffled_ckd = ckd.sample(with_replacement=False)
training = shuffled_ckd.take(np.arange(79))
testing = shuffled_ckd.take(np.arange(79, 158))

Now let’s construct our classifier based on the points in the training sample:
training.scatter('White Blood Cell Count', 'Glucose', group='Color')
plt.xlim(-2, 6)
plt.ylim(-2, 6);

We get the following classification regions and decision boundary:

Place the test data on this graph and you can see at once that while the classifier got almost all the points right, there are some mistakes. For
example, some blue points of the test set fall in the gold region of the classifier.
Some errors notwithstanding, it looks like the classifier does fairly well on the test set. Assuming that the original sample was drawn randomly from
the underlying population, the hope is that the classifier will perform with similar accuracy on the overall population, since the test set was chosen
randomly from the original sample.

17.3. Rows of Tables

Now that we have a qualitative understanding of nearest neighbor classification, it’s time to implement our classifier.
Until this chapter, we have worked mostly with single columns of tables. But now we have to see whether one individual is “close” to another. Data for
individuals are contained in rows of tables.
So let’s start by taking a closer look at rows.
Here is the original table ckd containing data on patients who were tested for chronic kidney disease.
ckd = Table.read_table(path_data + 'ckd.csv').relabeled('Blood Glucose Random',
'Glucose')

The data corresponding to the first patient is in row 0 of the table, consistent with Python’s indexing system. The Table method row accesses the row
by taking the index of the row as its argument:
ckd.row(0)

Row(Age=48, Blood Pressure=70, Specific Gravity=1.005, Albumin=4, Sugar=0, Red Blood

Cells='normal', Pus Cell='abnormal', Pus Cell clumps='present', Bacteria='notpresent',
Glucose=117, Blood Urea=56, Serum Creatinine=3.8, Sodium=111, Potassium=2.5,
Hemoglobin=11.2, Packed Cell Volume=32, White Blood Cell Count=6700, Red Blood Cell
Count=3.9, Hypertension='yes', Diabetes Mellitus='no', Coronary Artery Disease='no',
Appetite='poor', Pedal Edema='yes', Anemia='yes', Class=1)

Rows have their very own data type: they are row objects. Notice how the display shows not only the values in the row but also the labels of the
corresponding columns.
Rows are in general not arrays, as their elements can be of different types. For example, some of the elements of the row above are strings (like
'abnormal') and some are numerical. So the row can’t be converted into an array.

However, rows share some characteristics with arrays. You can use item to access a particular element of a row. For example, to access the Albumin
level of Patient 0, we can look at the labels in the printout of the row above to find that it’s item 3:
ckd.row(0).item(3)

17.3.1. Converting Rows to Arrays (When Possible)

Rows whose elements are all numerical (or all strings) can be converted to arrays. Converting a row to an array gives us access to arithmetic
operations and other nice NumPy functions, so it is often useful.
Recall that in the previous section we tried to classify the patients as ‘CKD’ or ‘not CKD’, based on two attributes Hemoglobin and Glucose, both
measured in standard units.
ckd = Table().with_columns(
'Hemoglobin', standard_units(ckd.column('Hemoglobin')),
'Glucose', standard_units(ckd.column('Glucose')),
'Class', ckd.column('Class')
)

color_table = Table().with_columns(
'Class', make_array(1, 0),
'Color', make_array('darkblue', 'gold')
)
ckd = ckd.join('Class', color_table)
ckd
Class Hemoglobin Glucose Color
0 0.456884 0.133751 gold
0 1.153 ‑0.947597 gold
0 0.770138 ‑0.762223 gold
0 0.596108 ‑0.190654 gold
0 ‑0.239236 ‑0.49961 gold
0 ‑0.0304002 ‑0.159758 gold
0 0.282854 ‑0.00527964 gold
0 0.108824 ‑0.623193 gold
0 0.0740178 ‑0.515058 gold
0 0.83975 ‑0.422371 gold
... (148 rows omitted)
Here is a scatter plot of the two attributes, along with a red point corresponding to Alice, a new patient. Her value of hemoglobin is 0 (that is, at the
average) and glucose 1.1 (that is, 1.1 SDs above average).
alice = make_array(0, 1.1)
ckd.scatter('Hemoglobin', 'Glucose', group='Color')
plots.scatter(alice.item(0), alice.item(1), color='red', s=30);

To find the distance between Alice’s point and any of the other points, we only need the values of the attributes:
ckd_attributes = ckd.select('Hemoglobin', 'Glucose')

ckd_attributes
Hemoglobin Glucose
0.456884 0.133751
1.153 ‑0.947597
0.770138 ‑0.762223
0.596108 ‑0.190654
‑0.239236 ‑0.49961
‑0.0304002 ‑0.159758
0.282854 ‑0.00527964
0.108824 ‑0.623193
0.0740178 ‑0.515058
0.83975 ‑0.422371
... (148 rows omitted)
Each row consists of the coordinates of one point in our training sample. Because the rows now consist only of numerical values, it is possible to
convert them to arrays. For this, we use the function np.array, which converts any kind of sequential object, like a row, to an array. (Our old friend
make_array is for creating arrays, not for converting other kinds of sequences to arrays.)

ckd_attributes.row(3)

Row(Hemoglobin=0.5961076648232668, Glucose=-0.19065363034327712)

np.array(ckd_attributes.row(3))

array([ 0.59610766, -0.19065363])

This is very handy because we can now use array operations on the data in each row.

17.3.2. Distance Between Points When There are Two Attributes

The main calculation we need to do is to find the distance between Alice’s point and any other point. For this, the first thing we need is a way to
compute the distance between any pair of points.
How do we do this? In 2‑dimensional space, it’s pretty easy. If we have a point at coordinates $(x_0,y_0)$ and another at $(x_1,y_1)$, the distance
between them is
\[ D = \sqrt{(x_0‑x_1)^2 + (y_0‑y_1)^2} \]
(Where did this come from? It comes from the Pythogorean theorem: we have a right triangle with side lengths $x_0‑x_1$ and $y_0‑y_1$, and we
want to find the length of the hypotenuse.)
In the next section we’ll see that this formula has a straightforward extension when there are more than two attributes. For now, let’s use the formula
and array operations to find the distance between Alice and the patient in Row 3.
patient3 = np.array(ckd_attributes.row(3))
alice, patient3

(array([0. , 1.1]), array([ 0.59610766, -0.19065363]))

distance = np.sqrt(np.sum((alice - patient3)**2))

distance

1.421664918881847

We’re going to need the distance between Alice and a bunch of points, so let’s write a function called distance that computes the distance between
any pair of points. The function will take two arrays, each containing the $(x, y)$ coordinates of a point. (Remember, those are really the Hemoglobin
and Glucose levels of a patient.)
def distance(point1, point2):
"""Returns the Euclidean distance between point1 and point2.

Each argument is an array containing the coordinates of a point."""

return np.sqrt(np.sum((point1 - point2)**2))

distance(alice, patient3)

1.421664918881847

We have begun to build our classifier: the distance function is the first building block. Now let’s work on the next piece.

17.3.3. Using apply on an Entire Row

Recall that if you want to apply a function to each element of a column of a table, one way to do that is by the call
table_name.apply(function_name, column_label). This evaluates to an array consisting of the values of the function when we call it on each
element of the column. So each entry of the array is based on the corresponding row of the table.
If you use apply without specifying a column label, then the entire row is passed to the function. Let’s see how this works on a very small table t
containing the information about the first five patients in the training sample.
t = ckd_attributes.take(np.arange(5))
t

Hemoglobin Glucose
0.456884 0.133751
1.153 ‑0.947597
0.770138 ‑0.762223
0.596108 ‑0.190654
‑0.239236 ‑0.49961
Just as an example, suppose that for each patient we want to know how unusual their most unusual attribute is. Concretely, if a patient’s hemoglobin
level is further from the average than her glucose level, we want to know how far it is from the average. If her glucose level is further from the average
than her hemoglobin level, we want to know how far that is from the average instead.
That’s the same as taking the maximum of the absolute values of the two quantities. To do this for a particular row, we can convert the row to an array
and use array operations.
def max_abs(row):
return np.max(np.abs(np.array(row)))

max_abs(t.row(4))

0.4996102825918697

And now we can apply max_abs to each row of the table t:

t.apply(max_abs)

array([0.4568837 , 1.15300352, 0.77013762, 0.59610766, 0.49961028])

This way of using apply will help us create the next building block of our classifier.

17.3.4. Alice’s $k$ Nearest Neighbors

If we want to classify Alice using a k‑nearest neighbor classifier, we have to identify her $k$ nearest neighbors. What are the steps in this process?
Suppose $k = 5$. Then the steps are:
Step 1. Find the distance between Alice and each point in the training sample.
Step 2. Sort the data table in increasing order of the distances.
Step 3. Take the top 5 rows of the sorted table.
Steps 2 and 3 seem straightforward, provided we have the distances. So let’s focus on Step 1.
Here’s Alice:
alice

array([0. , 1.1])

What we need is a function that finds the distance between Alice and another point whose coordinates are contained in a row. The function distance
returns the distance between any two points whose coordinates are in arrays. We can use that to define distance_from_alice, which takes a row as
its argument and returns the distance between that row and Alice.
def distance_from_alice(row):
"""Returns distance between Alice and a row of the attributes table"""
return distance(alice, np.array(row))

distance_from_alice(ckd_attributes.row(3))

1.421664918881847

Now we can apply the function distance_from_alice to each row of ckd_attributes, and augment the table ckd with the distances. Step 1 is
complete!
distances = ckd_attributes.apply(distance_from_alice)
ckd_with_distances = ckd.with_column('Distance from Alice', distances)

ckd_with_distances

Class Hemoglobin Glucose Color Distance from Alice

0 0.456884 0.133751 gold 1.06882
0 1.153 ‑0.947597 gold 2.34991
0 0.770138 ‑0.762223 gold 2.01519
0 0.596108 ‑0.190654 gold 1.42166
0 ‑0.239236 ‑0.49961 gold 1.6174
0 ‑0.0304002 ‑0.159758 gold 1.26012
0 0.282854 ‑0.00527964 gold 1.1409
0 0.108824 ‑0.623193 gold 1.72663
0 0.0740178 ‑0.515058 gold 1.61675
0 0.83975 ‑0.422371 gold 1.73862
... (148 rows omitted)
For Step 2, let’s sort the table in increasing order of distance:
sorted_by_distance = ckd_with_distances.sort('Distance from Alice')
sorted_by_distance
Class Hemoglobin Glucose Color Distance from Alice
1 0.83975 1.2151 darkblue 0.847601
1 ‑0.970162 1.27689 darkblue 0.986156
0 ‑0.0304002 0.0874074 gold 1.01305
0 0.14363 0.0874074 gold 1.02273
1 ‑0.413266 2.04928 darkblue 1.03534
0 0.387272 0.118303 gold 1.05532
0 0.456884 0.133751 gold 1.06882
0 0.178436 0.0410639 gold 1.07386
0 0.00440582 0.025616 gold 1.07439
0 ‑0.169624 0.025616 gold 1.08769
... (148 rows omitted)
Step 3: The top 5 rows correspond to Alice’s 5 nearest neighbors; you can replace 5 by any other positive integer.
alice_5_nearest_neighbors = sorted_by_distance.take(np.arange(5))
alice_5_nearest_neighbors

Class Hemoglobin Glucose Color Distance from Alice

1 0.83975 1.2151 darkblue 0.847601
1 ‑0.970162 1.27689 darkblue 0.986156
0 ‑0.0304002 0.0874074 gold 1.01305
0 0.14363 0.0874074 gold 1.02273
1 ‑0.413266 2.04928 darkblue 1.03534
Three of Alice’s five nearest neighbors are blue points and two are gold. So a 5‑nearest neighbor classifier would classify Alice as blue: it would
predict that Alice has chronic kidney disease.
The graph below zooms in on Alice and her five nearest neighbors. The two gold ones just inside the circle directly below the red point. The classifier
says Alice is more like the three blue ones around her.

We are well on our way to implementing our k‑nearest neighbor classifier. In the next two sections we will put it together and assess its accuracy.
17.4. Implementing the Classifier
We are now ready to implement a $k$‑nearest neighbor classifier based on multiple attributes. We have used only two attributes so far, for ease of
visualization. But usually predictions will be based on many attributes. Here is an example that shows how multiple attributes can be better than pairs.

17.4.1. Banknote authentication

This time we’ll look at predicting whether a banknote (e.g., a $20 bill) is counterfeit or legitimate. Researchers have put together a data set for us,
based on photographs of many individual banknotes: some counterfeit, some legitimate. They computed a few numbers from each image, using
techniques that we won’t worry about for this course. So, for each banknote, we know a few numbers that were computed from a photograph of it as
well as its class (whether it is counterfeit or not). Let’s load it into a table and take a look.
banknotes = Table.read_table(path_data + 'banknote.csv')
banknotes

WaveletVar WaveletSkew WaveletCurt Entropy Class

3.6216 8.6661 ‑2.8073 ‑0.44699 0
4.5459 8.1674 ‑2.4586 ‑1.4621 0
3.866 ‑2.6383 1.9242 0.10645 0
3.4566 9.5228 ‑4.0112 ‑3.5944 0
0.32924 ‑4.4552 4.5718 ‑0.9888 0
4.3684 9.6718 ‑3.9606 ‑3.1625 0
3.5912 3.0129 0.72888 0.56421 0
2.0922 ‑6.81 8.4636 ‑0.60216 0
3.2032 5.7588 ‑0.75345 ‑0.61251 0
1.5356 9.1772 ‑2.2718 ‑0.73535 0
... (1362 rows omitted)
Let’s look at whether the first two numbers tell us anything about whether the banknote is counterfeit or not. Here’s a scatterplot:
color_table = Table().with_columns(
'Class', make_array(1, 0),
'Color', make_array('darkblue', 'gold')
)

banknotes = banknotes.join('Class', color_table)

banknotes.scatter('WaveletVar', 'WaveletCurt', group='Color')

Pretty interesting! Those two measurements do seem helpful for predicting whether the banknote is counterfeit or not. However, in this example you
can now see that there is some overlap between the blue cluster and the gold cluster. This indicates that there will be some images where it’s hard to
tell whether the banknote is legitimate based on just these two numbers. Still, you could use a $k$‑nearest neighbor classifier to predict the
legitimacy of a banknote.
Take a minute and think it through: Suppose we used $k=11$ (say). What parts of the plot would the classifier get right, and what parts would it make
errors on? What would the decision boundary look like?
The patterns that show up in the data can get pretty wild. For instance, here’s what we’d get if used a different pair of measurements from the
images:
banknotes.scatter('WaveletSkew', 'Entropy', group='Color')

There does seem to be a pattern, but it’s a pretty complex one. Nonetheless, the $k$‑nearest neighbors classifier can still be used and will effectively
“discover” patterns out of this. This illustrates how powerful machine learning can be: it can effectively take advantage of even patterns that we
would not have anticipated, or that we would have thought to “program into” the computer.

17.4.2. Multiple attributes

So far I’ve been assuming that we have exactly 2 attributes that we can use to help us make our prediction. What if we have more than 2? For
instance, what if we have 3 attributes?
Here’s the cool part: you can use the same ideas for this case, too. All you have to do is make a 3‑dimensional scatterplot, instead of a 2‑dimensional
plot. You can still use the $k$‑nearest neighbors classifier, but now computing distances in 3 dimensions instead of just 2. It just works. Very cool!
In fact, there’s nothing special about 2 or 3. If you have 4 attributes, you can use the $k$‑nearest neighbors classifier in 4 dimensions. 5 attributes?
Work in 5‑dimensional space. And no need to stop there! This all works for arbitrarily many attributes; you just work in a very high dimensional space.
It gets wicked‑impossible to visualize, but that’s OK. The computer algorithm generalizes very nicely: all you need is the ability to compute the
distance, and that’s not hard. Mind‑blowing stuff!
For instance, let’s see what happens if we try to predict whether a banknote is counterfeit or not using 3 of the measurements, instead of just 2.
Here’s what you get:
ax = plt.figure(figsize=(8,8)).add_subplot(111, projection='3d')
ax.scatter(banknotes.column('WaveletSkew'),
banknotes.column('WaveletVar'),
banknotes.column('WaveletCurt'),
c=banknotes.column('Color'));
Awesome! With just 2 attributes, there was some overlap between the two clusters (which means that the classifier was bound to make some
mistakes for pointers in the overlap). But when we use these 3 attributes, the two clusters have almost no overlap. In other words, a classifier that
uses these 3 attributes will be more accurate than one that only uses the 2 attributes.
This is a general phenomenom in classification. Each attribute can potentially give you new information, so more attributes sometimes helps you build
a better classifier. Of course, the cost is that now we have to gather more information to measure the value of each attribute, but this cost may be
well worth it if it significantly improves the accuracy of our classifier.
To sum up: you now know how to use $k$‑nearest neighbor classification to predict the answer to a yes/no question, based on the values of some
attributes, assuming you have a training set with examples where the correct prediction is known. The general roadmap is this:
1. identify some attributes that you think might help you predict the answer to the question.
2. Gather a training set of examples where you know the values of the attributes as well as the correct prediction.
3. To make predictions in the future, measure the value of the attributes and then use $k$‑nearest neighbor classification to predict the answer to
the question.

17.4.3. Distance in Multiple Dimensions

We know how to compute distance in 2‑dimensional space. If we have a point at coordinates $(x_0,y_0)$ and another at $(x_1,y_1)$, the distance
between them is
\[D = \sqrt{(x_0‑x_1)^2 + (y_0‑y_1)^2}.\]
In 3‑dimensional space, the points are $(x_0, y_0, z_0)$ and $(x_1, y_1, z_1)$, and the formula for the distance between them is
\[ D = \sqrt{(x_0‑x_1)^2 + (y_0‑y_1)^2 + (z_0‑z_1)^2} \]
In $n$‑dimensional space, things are a bit harder to visualize, but I think you can see how the formula generalized: we sum up the squares of the
differences between each individual coordinate, and then take the square root of that.
In the last section, we defined the function distance which returned the distance between two points. We used it in two‑dimensions, but the great
news is that the function doesn’t care how many dimensions there are! It just subtracts the two arrays of coordinates (no matter how long the arrays
are), squares the differences and adds up, and then takes the square root. To work in multiple dimensions, we don’t have to change the code at all.
def distance(point1, point2):
"""Returns the distance between point1 and point2
where each argument is an array
consisting of the coordinates of the point"""
return np.sqrt(np.sum((point1 - point2)**2))

Let’s use this on a new dataset. The table wine contains the chemical composition of 178 different Italian wines. The classes are the grape species,
called cultivars. There are three classes but let’s just see whether we can tell Class 1 apart from the other two.
wine = Table.read_table(path_data + 'wine.csv')

# For converting Class to binary

def is_one(x):
if x == 1:
return 1
else:
return 0

wine = wine.with_column('Class', wine.apply(is_one, 0))

wine

Class Alcohol Malic Alcalinity

Acid Ash of Ash Magnesium Phenols Flavanoids
Total Nonflavanoid
phenols
1 14.23 1.71 2.43 15.6 127 2.8 3.06 0.28
1 13.2 1.78 2.14 11.2 100 2.65 2.76 0.26
1 13.16 2.36 2.67 18.6 101 2.8 3.24 0.3
1 14.37 1.95 2.5 16.8 113 3.85 3.49 0.24
1 13.24 2.59 2.87 21 118 2.8 2.69 0.39
1 14.2 1.76 2.45 15.2 112 3.27 3.39 0.34
1 14.39 1.87 2.45 14.6 96 2.5 2.52 0.3
1 14.06 2.15 2.61 17.6 121 2.6 2.51 0.31
1 14.83 1.64 2.17 14 97 2.8 2.98 0.29
1 13.86 1.35 2.27 16 98 2.98 3.15 0.22
... (168 rows omitted)
The first two wines are both in Class 1. To find the distance between them, we first need a table of just the attributes:
wine_attributes = wine.drop('Class')

distance(np.array(wine_attributes.row(0)), np.array(wine_attributes.row(1)))

31.265012394048398

The last wine in the table is of Class 0. Its distance from the first wine is:
distance(np.array(wine_attributes.row(0)), np.array(wine_attributes.row(177)))

506.05936766351834

That’s quite a bit bigger! Let’s do some visualization to see if Class 1 really looks different from Class 0.
wine_with_colors = wine.join('Class', color_table)

wine_with_colors.scatter('Flavanoids', 'Alcohol', group='Color')

The blue points (Class 1) are almost entirely separate from the gold ones. That is one indication of why the distance between two Class 1 wines would
be smaller than the distance between wines of two different classes. We can see a similar phenomenon with a different pair of attributes too:
wine_with_colors.scatter('Alcalinity of Ash', 'Ash', group='Color')

But for some pairs the picture is more murky.

wine_with_colors.scatter('Magnesium', 'Total Phenols', group='Color')

Let’s see if we can implement a classifier based on all of the attributes. After that, we’ll see how accurate it is.

17.4.4. A Plan for the Implementation

It’s time to write some code to implement the classifier. The input is a point that we want to classify. The classifier works by finding the $k$ nearest
neighbors of point from the training set. So, our approach will go like this:
1. Find the closest $k$ neighbors of point, i.e., the $k$ wines from the training set that are most similar to point.
2. Look at the classes of those $k$ neighbors, and take the majority vote to find the most‑common class of wine. Use that as our predicted class
for point.
So that will guide the structure of our Python code.
def closest(training, p, k):
...

def majority(topkclasses):
...

def classify(training, p, k):

kclosest = closest(training, p, k)
kclosest.classes = kclosest.select('Class')
return majority(kclosest)

17.4.5. Implementation Step 1

To implement the first step for the kidney disease data, we had to compute the distance from each patient in the training set to point, sort them by
distance, and take the $k$ closest patients in the training set.
That’s what we did in the previous section with the point corresponding to Alice. Let’s generalize that code. We’ll redefine distance here, just for
convenience.
def distance(point1, point2):
"""Returns the distance between point1 and point2
where each argument is an array
consisting of the coordinates of the point"""
return np.sqrt(np.sum((point1 - point2)**2))

def all_distances(training, new_point):

"""Returns an array of distances
between each point in the training set
and the new point (which is a row of attributes)"""
attributes = training.drop('Class')
def distance_from_point(row):
return distance(np.array(new_point), np.array(row))
return attributes.apply(distance_from_point)

def table_with_distances(training, new_point):

"""Augments the training table
with a column of distances from new_point"""
return training.with_column('Distance', all_distances(training, new_point))

def closest(training, new_point, k):

"""Returns a table of the k rows of the augmented table
corresponding to the k smallest distances"""
with_dists = table_with_distances(training, new_point)
sorted_by_distance = with_dists.sort('Distance')
topk = sorted_by_distance.take(np.arange(k))
return topk

Let’s see how this works on our wine data. We’ll just take the first wine and find its five nearest neighbors among all the wines. Remember that since
this wine is part of the dataset, it is its own nearest neighbor. So we should expect to see it at the top of the list, followed by four others.
First let’s extract its attributes:
special_wine = wine.drop('Class').row(0)

And now let’s find its 5 nearest neighbors.

closest(wine, special_wine, 5)
Class Alcohol Malic Alcalinity
Acid Ash of Ash Magnesium Phenols Flavanoids
Total Nonflavanoid
phenols
1 14.23 1.71 2.43 15.6 127 2.8 3.06 0.28
1 13.74 1.67 2.25 16.4 118 2.6 2.9 0.21
1 14.21 4.04 2.44 18.9 111 2.85 2.65 0.3
1 14.1 2.02 2.4 18.8 103 2.75 2.92 0.32
1 14.38 3.59 2.28 16 102 3.25 3.17 0.27
Bingo! The first row is the nearest neighbor, which is itself – there’s a 0 in the Distance column as expected. All five nearest neighbors are of Class 1,
which is consistent with our earlier observation that Class 1 wines appear to be clumped together in some dimensions.

17.4.6. Implementation Steps 2 and 3

Next we need to take a “majority vote” of the nearest neighbors and assign our point the same class as the majority.
def majority(topkclasses):
ones = topkclasses.where('Class', are.equal_to(1)).num_rows
zeros = topkclasses.where('Class', are.equal_to(0)).num_rows
if ones > zeros:
return 1
else:
return 0

def classify(training, new_point, k):

closestk = closest(training, new_point, k)
topkclasses = closestk.select('Class')
return majority(topkclasses)

classify(wine, special_wine, 5)

If we change special_wine to be the last one in the dataset, is our classifier able to tell that it’s in Class 0?
special_wine = wine.drop('Class').row(177)
classify(wine, special_wine, 5)

Yes! The classifier gets this one right too.

But we don’t yet know how it does with all the other wines, and in any case we know that testing on wines that are already part of the training set
might be over‑optimistic. In the final section of this chapter, we will separate the wines into a training and test set and then measure the accuracy of
our classifier on the test set.

17.5. The Accuracy of the Classifier

To see how well our classifier does, we might put 50% of the data into the training set and the other 50% into the test set. Basically, we are setting
aside some data for later use, so we can use it to measure the accuracy of our classifier. We’ve been calling that the test set. Sometimes people will
call the data that you set aside for testing a hold‑out set, and they’ll call this strategy for estimating accuracy the hold‑out method.
Note that this approach requires great discipline. Before you start applying machine learning methods, you have to take some of your data and set it
aside for testing. You must avoid using the test set for developing your classifier: you shouldn’t use it to help train your classifier or tweak its settings
or for brainstorming ways to improve your classifier. Instead, you should use it only once, at the very end, after you’ve finalized your classifier, when
you want an unbiased estimate of its accuracy.

17.5.1. Measuring the Accuracy of Our Wine Classifier

OK, so let’s apply the hold‑out method to evaluate the effectiveness of the $k$‑nearest neighbor classifier for identifying wines. The data set has 178
wines, so we’ll randomly permute the data set and put 89 of them in the training set and the remaining 89 in the test set.
shuffled_wine = wine.sample(with_replacement=False)
training_set = shuffled_wine.take(np.arange(89))
test_set = shuffled_wine.take(np.arange(89, 178))

We’ll train the classifier using the 89 wines in the training set, and evaluate how well it performs on the test set. To make our lives easier, we’ll write a
function to evaluate a classifier on every wine in the test set:
def count_zero(array):
"""Counts the number of 0's in an array"""
return len(array) - np.count_nonzero(array)

def count_equal(array1, array2):

"""Takes two numerical arrays of equal length
and counts the indices where the two are equal"""
return count_zero(array1 - array2)

def evaluate_accuracy(training, test, k):

test_attributes = test.drop('Class')
def classify_testrow(row):
return classify(training, row, k)
c = test_attributes.apply(classify_testrow)
return count_equal(c, test.column('Class')) / test.num_rows

Now for the grand reveal – let’s see how we did. We’ll arbitrarily use $k=5$.
evaluate_accuracy(training_set, test_set, 5)

0.898876404494382

The accuracy rate isn’t bad at all for a simple classifier.

17.5.2. Breast Cancer Diagnosis

Now I want to do an example based on diagnosing breast cancer. I was inspired by Brittany Wenger, who won the Google national science fair in 2012
as a 17‑year old high school student. Here’s Brittany:

Brittany’s science fair project was to build a classification algorithm to diagnose breast cancer. She won grand prize for building an algorithm whose
accuracy was almost 99%.
Let’s see how well we can do, with the ideas we’ve learned in this course.
So, let me tell you a little bit about the data set. Basically, if a woman has a lump in her breast, the doctors may want to take a biopsy to see if it is
cancerous. There are several different procedures for doing that. Brittany focused on fine needle aspiration (FNA), because it is less invasive than the
alternatives. The doctor gets a sample of the mass, puts it under a microscope, takes a picture, and a trained lab tech analyzes the picture to
determine whether it is cancer or not. We get a picture like one of the following:
Unfortunately, distinguishing between benign vs malignant can be tricky. So, researchers have studied the use of machine learning to help with this
task. The idea is that we’ll ask the lab tech to analyze the image and compute various attributes: things like the typical size of a cell, how much
variation there is among the cell sizes, and so on. Then, we’ll try to use this information to predict (classify) whether the sample is malignant or not.
We have a training set of past samples from women where the correct diagnosis is known, and we’ll hope that our machine learning algorithm can
use those to learn how to predict the diagnosis for future samples.
We end up with the following data set. For the “Class” column, 1 means malignant (cancer); 0 means benign (not cancer).
patients = Table.read_table(path_data + 'breast-cancer.csv').drop('ID')
patients

Clump Uniformity
of Cell
Uniformity Marginal Single Bare
of Cell Adhesion Epithelial Nuclei Chromatin Bland Normal
Thickness Size Shape Cell Size Nucleoli
5 1 1 1 2 1 3 1
5 4 4 5 7 10 3 2
3 1 1 1 2 2 3 1
6 8 8 1 3 4 3 7
4 1 1 3 2 1 3 1
8 10 10 8 7 10 9 7
1 1 1 1 2 10 3 1
2 1 2 1 2 1 3 1
2 1 1 1 2 1 1 1
4 2 1 1 2 1 2 1
... (673 rows omitted)
So we have 9 different attributes. I don’t know how to make a 9‑dimensional scatterplot of all of them, so I’m going to pick two and plot them:
color_table = Table().with_columns(
'Class', make_array(1, 0),
'Color', make_array('darkblue', 'gold')
)
patients_with_colors = patients.join('Class', color_table)
patients_with_colors.scatter('Bland Chromatin', 'Single Epithelial Cell Size',
group='Color')

Oops. That plot is utterly misleading, because there are a bunch of points that have identical values for both the x‑ and y‑coordinates. To make it
easier to see all the data points, I’m going to add a little bit of random jitter to the x‑ and y‑values. Here’s how that looks:

For instance, you can see there are lots of samples with chromatin = 2 and epithelial cell size = 2; all non‑cancerous.
Keep in mind that the jittering is just for visualization purposes, to make it easier to get a feeling for the data. We’re ready to work with the data now,
and we’ll use the original (unjittered) data.
First we’ll create a training set and a test set. The data set has 683 patients, so we’ll randomly permute the data set and put 342 of them in the
training set and the remaining 341 in the test set.
shuffled_patients = patients.sample(683, with_replacement=False)
training_set = shuffled_patients.take(np.arange(342))
test_set = shuffled_patients.take(np.arange(342, 683))

Let’s stick with 5 nearest neighbors, and see how well our classifier does.
evaluate_accuracy(training_set, test_set, 5)

0.967741935483871

Over 96% accuracy. Not bad! Once again, pretty darn good for such a simple technique.
As a footnote, you might have noticed that Brittany Wenger did even better. What techniques did she use? One key innovation is that she
incorporated a confidence score into her results: her algorithm had a way to determine when it was not able to make a confident prediction, and for
those patients, it didn’t even try to predict their diagnosis. Her algorithm was 99% accurate on the patients where it made a prediction – so that
extension seemed to help quite a bit.
17.6. Multiple Regression
Now that we have explored ways to use multiple attributes to predict a categorical variable, let us return to predicting a quantitative variable.
Predicting a numerical quantity is called regression, and a commonly used method to use multiple attributes for regression is called multiple linear
regression.

17.6.1. Home Prices

The following dataset of house prices and attributes was collected over several years for the city of Ames, Iowa. A description of the dataset appears
online. We will focus only a subset of the columns. We will try to predict the sale price column from the other columns.
all_sales = Table.read_table(path_data + 'house.csv')
sales = all_sales.where('Bldg Type', '1Fam').where('Sale Condition', 'Normal').select(
'SalePrice', '1st Flr SF', '2nd Flr SF',
'Total Bsmt SF', 'Garage Area',
'Wood Deck SF', 'Open Porch SF', 'Lot Area',
'Year Built', 'Yr Sold')
sales.sort('SalePrice')

1st 2nd Total Garage Wood Open Lot Year Yr

SalePrice Flr Flr SF Bsmt SF Area Deck SF Porch SF Area Built Sold
SF
35000 498 0 498 216 0 0 8088 1922 2006
39300 334 0 0 0 0 0 5000 1946 2007
40000 649 668 649 250 0 54 8500 1920 2008
45000 612 0 0 308 0 0 5925 1940 2009
52000 729 0 270 0 0 0 4130 1935 2008
52500 693 0 693 0 0 20 4118 1941 2006
55000 723 363 723 400 0 24 11340 1920 2008
55000 796 0 796 0 0 0 3636 1922 2008
57625 810 0 0 280 119 24 21780 1910 2009
58500 864 0 864 200 0 0 8212 1914 2010
... (1992 rows omitted)
A histogram of sale prices shows a large amount of variability and a distribution that is clearly not normal. A long tail to the right contains a few
houses that had very high prices. The short left tail does not contain any houses that sold for less than $35,000.
sales.hist('SalePrice', bins=32, unit='$')

17.6.1.1. Correlation
No single attribute is sufficient to predict the sale price. For example, the area of first floor, measured in square feet, correlates with sale price but
only explains some of its variability.
sales.scatter('1st Flr SF', 'SalePrice')

correlation(sales, 'SalePrice', '1st Flr SF')

0.6424662541030225

In fact, none of the individual attributes have a correlation with sale price that is above 0.7 (except for the sale price itself).
for label in sales.labels:
print('Correlation of', label, 'and SalePrice:\t', correlation(sales, label,
'SalePrice'))

Correlation of SalePrice and SalePrice: 1.0

Correlation of 1st Flr SF and SalePrice: 0.6424662541030225
Correlation of 2nd Flr SF and SalePrice: 0.3575218942800824
Correlation of Total Bsmt SF and SalePrice: 0.652978626757169
Correlation of Garage Area and SalePrice: 0.6385944852520443
Correlation of Wood Deck SF and SalePrice: 0.3526986661950492
Correlation of Open Porch SF and SalePrice: 0.3369094170263733
Correlation of Lot Area and SalePrice: 0.2908234551157694
Correlation of Year Built and SalePrice: 0.5651647537135916
Correlation of Yr Sold and SalePrice: 0.02594857908072111

However, combining attributes can provide higher correlation. In particular, if we sum the first floor and second floor areas, the result has a higher
correlation than any single attribute alone.
both_floors = sales.column(1) + sales.column(2)
correlation(sales.with_column('Both Floors', both_floors), 'SalePrice', 'Both Floors')

0.7821920556134877

This high correlation indicates that we should try to use more than one attribute to predict the sale price. In a dataset with multiple observed
attributes and a single numerical value to be predicted (the sale price in this case), multiple linear regression can be an effective technique.

17.6.2. Multiple Linear Regression

In multiple linear regression, a numerical output is predicted from numerical input attributes by multiplying each attribute value by a different slope,
then summing the results. In this example, the slope for the 1st Flr SF would represent the dollars per square foot of area on the first floor of the
house that should be used in our prediction.
Before we begin prediction, we split our data randomly into a training and test set of equal size.
train, test = sales.split(1001)
print(train.num_rows, 'training and', test.num_rows, 'test instances.')

1001 training and 1001 test instances.

The slopes in multiple regression is an array that has one slope value for each attribute in an example. Predicting the sale price involves multiplying
each attribute by the slope and summing the result.
def predict(slopes, row):
return sum(slopes * np.array(row))

example_row = test.drop('SalePrice').row(0)
print('Predicting sale price for:', example_row)
example_slopes = np.random.normal(10, 1, len(example_row))
print('Using slopes:', example_slopes)
print('Result:', predict(example_slopes, example_row))

Predicting sale price for: Row(1st Flr SF=1207, 2nd Flr SF=0, Total Bsmt SF=1135.0,
Garage Area=264.0, Wood Deck SF=0, Open Porch SF=240, Lot Area=9510, Year Built=1962, Yr
Sold=2006)
Using slopes: [ 9.52065867 8.58939769 11.48702417 9.50389131 9.09151019 9.86944284
10.71929443 10.88966608 8.33339346]
Result: 169429.7032316262

The result is an estimated sale price, which can be compared to the actual sale price to assess whether the slopes provide accurate predictions.
Since the example_slopes above were chosen at random, we should not expect them to provide accurate predictions at all.
print('Actual sale price:', test.column('SalePrice').item(0))
print('Predicted sale price using random slopes:', predict(example_slopes, example_row))

Actual sale price: 147000

Predicted sale price using random slopes: 169429.7032316262

17.6.2.1. Least Squares Regression

The next step in performing multiple regression is to define the least squares objective. We perform the prediction for each row in the training set,
and then compute the root mean squared error (RMSE) of the predictions from the actual prices.
train_prices = train.column(0)
train_attributes = train.drop(0)

def rmse(slopes, attributes, prices):

errors = []
for i in np.arange(len(prices)):
predicted = predict(slopes, attributes.row(i))
actual = prices.item(i)
errors.append((predicted - actual) ** 2)
return np.mean(errors) ** 0.5

def rmse_train(slopes):
return rmse(slopes, train_attributes, train_prices)

print('RMSE of all training examples using random slopes:', rmse_train(example_slopes))

RMSE of all training examples using random slopes: 68153.56796456952

Finally, we use the minimize function to find the slopes with the lowest RMSE. Since the function we want to minimize, rmse_train, takes an array
instead of a number, we must pass the array=True argument to minimize. When this argument is used, minimize also requires an initial guess of the
slopes so that it knows the dimension of the input array. Finally, to speed up optimization, we indicate that rmse_train is a smooth function using the
smooth=True attribute. Computation of the best slopes may take several minutes.

best_slopes = minimize(rmse_train, start=example_slopes, smooth=True, array=True)

print('The best slopes for the training set:')
Table(train_attributes.labels).with_row(list(best_slopes)).show()
print('RMSE of all training examples using the best slopes:', rmse_train(best_slopes))
The best slopes for the training set:

1st Flr 2nd Flr Total Garage Wood Porch Open Year Yr Sold
SF SF Bsmt SF Area Deck SF Lot Area Built
SF
68.7068 74.3857 56.0494 36.1706 26.4397 21.4779 0.558904 534.101 ‑528.216
RMSE of all training examples using the best slopes: 29311.117940347867

17.6.2.2. Interpreting Multiple Regression

Let’s interpret these results. The best slopes give us a method for estimating the price of a house from its attributes. A square foot of area on the first
floor is worth about $75 (the first slope), while one on the second floor is worth about $70 (the second slope). The final negative value describes the
market: prices in later years were lower on average.
The RMSE of around $30,000 means that our best linear prediction of the sale price based on all of the attributes is off by around $30,000 on the
training set, on average. We find a similar error when predicting prices on the test set, which indicates that our prediction method will generalize to
other samples from the same population.
test_prices = test.column(0)
test_attributes = test.drop(0)

def rmse_test(slopes):
return rmse(slopes, test_attributes, test_prices)

rmse_linear = rmse_test(best_slopes)
print('Test set RMSE for multiple linear regression:', rmse_linear)

Test set RMSE for multiple linear regression: 33025.064938240575

If the predictions were perfect, then a scatter plot of the predicted and actual values would be a straight line with slope 1. We see that most dots fall
near that line, but there is some error in the predictions.
def fit(row):
return sum(best_slopes * np.array(row))

test.with_column('Fitted', test.drop(0).apply(fit)).scatter('Fitted', 0)
plots.plot([0, 5e5], [0, 5e5]);

A residual plot for multiple regression typically compares the errors (residuals) to the actual values of the predicted variable. We see in the residual
plot below that we have systematically underestimated the value of expensive houses, shown by the many positive residual values on the right side of
the graph.
test.with_column('Residual', test_prices-test.drop(0).apply(fit)).scatter(0, 'Residual')
plots.plot([0, 7e5], [0, 0]);
As with simple linear regression, interpreting the result of a predictor is at least as important as making predictions. There are many lessons about
interpreting multiple regression that are not included in this textbook. A natural next step after completing this text would be to study linear modeling
and regression in further depth.

17.6.3. Nearest Neighbors for Regression

Another approach to predicting the sale price of a house is to use the price of similar houses. This nearest neighbor approach is very similar to our
classifier. To speed up computation, we will only use the attributes that had the highest correlation with the sale price in our original analysis.
train_nn = train.select(0, 1, 2, 3, 4, 8)
test_nn = test.select(0, 1, 2, 3, 4, 8)
train_nn.show(3)

SalePrice 1st Flr SF 2nd Flr SF Total Bsmt SF Garage Area Year Built
270000 1673 0 1673 583 2000
158000 986 537 1067 295 1949
249000 1506 0 1494 672 2005
... (998 rows omitted)
The computation of closest neighbors is identical to a nearest‑neighbor classifier. In this case, we will exclude the 'SalePrice' rather than the
'Class' column from the distance computation. The five nearest neighbors of the first test row are shown below.

def distance(pt1, pt2):

"""The distance between two points, represented as arrays."""
return np.sqrt(sum((pt1 - pt2) ** 2))

def row_distance(row1, row2):

"""The distance between two rows of a table."""
return distance(np.array(row1), np.array(row2))

def distances(training, example, output):

"""Compute the distance from example for each row in training."""
dists = []
attributes = training.drop(output)
for row in attributes.rows:
dists.append(row_distance(row, example))
return training.with_column('Distance', dists)

def closest(training, example, k, output):

"""Return a table of the k closest neighbors to example."""
return distances(training, example, output).sort('Distance').take(np.arange(k))

example_nn_row = test_nn.drop(0).row(0)
closest(train_nn, example_nn_row, 5, 'SalePrice')
SalePrice 1st Flr SF 2nd Flr SF Total Bsmt SF Garage Area Year Built Distance
137000 1176 0 1158 303 1958 55.0182
146000 1150 0 1150 288 1961 63.6475
126175 1163 0 1162 220 1955 68.1909
157900 1188 0 1188 312 1962 73.9865
150000 1144 0 1169 286 1956 75.1332
One simple method for predicting the price is to average the prices of the nearest neighbors.
def predict_nn(example):
"""Return the majority class among the k nearest neighbors."""
return np.average(closest(train_nn, example, 5, 'SalePrice').column('SalePrice'))

predict_nn(example_nn_row)

143415.0

Finally, we can inspect whether our prediction is close to the true sale price for our one test example. Looks reasonable!
print('Actual sale price:', test_nn.column('SalePrice').item(0))
print('Predicted sale price using nearest neighbors:', predict_nn(example_nn_row))

Actual sale price: 147000

Predicted sale price using nearest neighbors: 143415.0

17.6.3.1. Evaluation
To evaluate the performance of this approach for the whole test set, we apply predict_nn to each test example, then compute the root mean squared
error of the predictions. Computation of the predictions may take several minutes.
nn_test_predictions = test_nn.drop('SalePrice').apply(predict_nn)
rmse_nn = np.mean((test_prices - nn_test_predictions) ** 2) ** 0.5

print('Test set RMSE for multiple linear regression: ', rmse_linear)

print('Test set RMSE for nearest neighbor regression:', rmse_nn)

Test set RMSE for multiple linear regression: 33025.064938240575

Test set RMSE for nearest neighbor regression: 36067.116043510105

For these data, the errors of the two techniques are quite similar! For different data sets, one technique might outperform another. By computing the
RMSE of both techniques on the same data, we can compare methods fairly. One note of caution: the difference in performance might not be due to
the technique at all; it might be due to the random variation due to sampling the training and test sets in the first place.
Finally, we can draw a residual plot for these predictions. We still underestimate the prices of the most expensive houses, but the bias does not
appear to be as systematic. However, fewer residuals are very close to zero, indicating that fewer prices were predicted with very high accuracy.
test.with_column('Residual', test_prices-nn_test_predictions).scatter(0, 'Residual')
plots.plot([0, 7e5], [0, 0]);
18. Updating Predictions
We know how to use training data to classify a point into one of two categories. Our classification is just a prediction of the class, based on the most
common class among the training points that are nearest our new point.
Suppose that we eventually find out the true class of our new point. Then we will know whether we got the classification right. Also, we will have a
new point that we can add to our training set, because we know its class. This updates our training set. So, naturally, we will want to update our
classifier based on the new training set.
This chapter looks at some simple scenarios where new data leads us to update our predictions. While the examples in the chapter are simple in
terms of calculation, the method of updating can be generalized to work in complex settings and is one of the most powerful tools used for machine
learning.

18.1. A “More Likely Than Not” Binary Classifier

Let’s try to use data to classify a point into one of two categories, choosing the category that we think is more likely than not. To do this, we not only
need the data but also a clear description of how chances are involved.
We will start out in a simple artifical setting just to develop the main technique, and then move to a more intriguing example.
Suppose there is a university class with the following composition:
60% of the students are Second Years and the remaining 40% are Third Years
50% of the Second Years have declared their major
80% of the Third Years have declared their major
Now suppose I pick a student at random from the class. Can you classify the student as Second Year or Third Year, using our “more likely than not”
criterion?
You can, because the student is picked at random and so you know that the chance that the student is a Second Year is 60%. That’s greater than the
40% chance of being a Third Year, so you would classify the student as Second Year.
The information about the majors is irrelevant, as we already know the proportions of Second and Third Years in the class.
We have a pretty simple classifier! But now suppose I give you some additional information about the student who was picked:
The student has declared a major.
Would this knowledge change your classification?

18.1.1. Updating the Prediction Based on New Information

Now that we know the student has declared a major, it becomes important to look at the relation between year and major declaration. It’s still true
that more students are Second Years than Third Years. But it’s also true that among the Third Years, a much higher percent have declared their major
than among the Second Years. Our classifier has to take both of these observations into account.
To visualize this, we will use a table students that consists of one row for each of 100 students whose years and majors have the same proportions as
given in the data.
students.show(3)

Year Major
Second Undeclared
Second Undeclared
Second Undeclared
... (97 rows omitted)
To check that the proportions are correct, let’s use pivot to cross‑classify each student according to the two variables.
students.pivot('Major', 'Year')

Year Declared Undeclared

Second 30 30
Third 32 8
The total count is 100 students, of whom 60 are Second Years and 40 are Third Years. Among the Second Years, 50% are in each of the Major
categories. Among the 40 Third Years, 20% are Undeclared and 80% Declared. So this population of 100 students has the same proportions as the
class in our problem, and we can assume that our student has been picked at random from among all 100 students.
We have to pick which row the student is most likely to be in. When we knew nothing more about the student, he or she could be in any of the four
cells, and therefore were more likely to be in the top row (Second Year) because that contains more students.
But now we know that the student has declared a major, so the space of possible outcomes has decreased: now the student can only be in one of the
two Declared cells.
There are 62 students in those cells, and 32 out of the 62 are Third Years. That’s more than half, even though not by much.
So, in the light of the new information about the student’s major, we have to update our prediction and now classify the student as a Third Year.
What is the chance that our classification is correct? We will be right for all the 32 Third Years who are Declared, and wrong for the 30 Second Years
who are Declared. The chance that we are correct is therefore about 0.516.
In other words, the chance that we are correct is the proportion of Third Years among the students who have Declared.
32/(30+32)

0.5161290322580645

18.1.2. Tree Diagram

The proportion that we have just calculated was based on a class of 100 students. But there’s no reason the class couldn’t have had 200 students, for
example, as long as all the proportions in the cells were correct. Then our calculation would just have been 64/(60 + 64) which is 0.516 as before.
So the calculation depends only on the proportions in the different categories, not on the counts. The proportions can be visualized in a tree diagram,
shown directly below the pivot table for ease of comparison.
students.pivot('Major', 'Year')

Year Declared Undeclared

Second 30 30
Third 32 8
Like the pivot table, this diagram partitions the students into four distinct groups known as “branches”. Notice that the “Third Year, Declared” branch
contains the proportion 0.4 x 0.8 = 0.32 of the students, corresponding to the 32 students in the “Third Year, Declared” cell of the pivot table. The
“Second Year, Declared” branch contains 0.6 x 0.5 = 0.3 of the students, corresponding to the 30 in the “Second Year, Declared” cell of the pivot
table.
We know that the student who was picked belongs to a “Declared” branch; that is, the student is either in the top branch or the third from top. Those
two branches now form our reduced space of possibilities, and all chances have to be calculated relative to the total chance of this reduced space.
So, given that the student is Declared, the chance of them being a Third Year can be calculated directly from the tree. The answer is the proportion in
the “Third Year, Declared” branch relative to the total proportion in the two “Declared” branches.
That is, the answer is the proportion of Third Years among students who are Declared, as before.
(0.4 * 0.8)/(0.6 * 0.5 + 0.4 * 0.8)

0.5161290322580645

18.1.3. Bayes’ Rule

The method that we have just used is due to the Reverend Thomas Bayes (1701‑1761). His method solved what was called an “inverse probability”
problem: given new data, how can you update chances you had found earlier? Though Bayes lived three centuries ago, his method is widely used
now in machine learning.
We will state the rule in the context of our population of students. First, some terminology:
Prior probabilities. Before we knew the chosen student’s major declaration status, the chance that the student was a Second Year was 60% and the
chance that the student was a Third Year was 40%. These are the prior probabilities of the two categories.
Likelihoods. These are the chances of the Major status, given the category of student; thus they can be read off the tree diagram. For example, the
likelihood of Declared status given that the student is a Second Year is 0.5.
Posterior probabilities. These are the chances of the two Year categories, after we have taken into account information about the Major declaration
status. We computed one of these:
The posterior probability that the student is a Third Year, given that the student has Declared, is denoted $P(\text{Third Year} ~\big{\vert}~
\text{Declared})$ and is calculated as follows.
\[\begin{split} \begin{align*} P(\mbox{Third Year} ~\big{\vert}~ \mbox{Declared}) ~ &=~ \frac{ 0.4 \times 0.8}{0.6 \times 0.5 ~+~ 0.4 \times 0.8} \\ \\
&=~ \frac{\mbox{(prior probability of Third Year)} \times \mbox{(likelihood of Declared given Third Year)}} {\mbox{total probability of Declared}}
\end{align*} \end{split}\]
The other posterior probability is
\[\begin{split} \begin{align*} P(\mbox{Second Year} ~\big{\vert}~ \mbox{Declared}) ~ &=~ \frac{ 0.6 \times 0.5}{0.6 \times 0.5 ~+~ 0.4 \times 0.8} \\ \\
&=~ \frac{\mbox{(prior probability of Second Year)} \times \mbox{(likelihood of Declared given Second Year)}} {\mbox{total probability of Declared}}
\end{align*} \end{split}\]
(0.6 * 0.5)/(0.6 * 0.5 + 0.4 * 0.8)

0.4838709677419354

That’s about 0.484, which is less than half, consistent with our classification of Third Year.
Notice that both the posterior probabilities have the same denominator: the chance of the new information, which is that the student has Declared.
Because of this, Bayes’ method is sometimes summarized as a statement about proportionality:
\[ \mbox{posterior} ~ \propto ~ \mbox{prior} \times \mbox{likelihood} \]
Formulas are great for efficiently describing calculations. But in settings like our example about students, it is simpler not to think in terms of
formulas. Just use the tree diagram.

18.2. Making Decisions

A primary use of Bayes’ Rule is to make decisions based on incomplete information, incorporating new information as it comes in. This section points
out the importance of keeping your assumptions in mind as you make decisions.
Many medical tests for diseases return Positive or Negative results. A Positive result means that according to the test, the patient has the disease. A
Negative result means the test concludes that the patient doesn’t have the disease.
Medical tests are carefully designed to be very accurate. But few tests are accurate 100% of the time. Almost all tests make errors of two kinds:
A false positive is an error in which the test concludes Positive but the patient doesn’t have the disease.
A false negative is an error in which the test concludes Negative but the patient does have the disease.
These errors can affect people’s decisions. False positives can cause anxiety and unnecessary treatment (which in some cases is expensive or
dangerous). False negatives can have even more serious consequences if the patient doesn’t receive treatment because of their Negative test result.

18.2.1. A Test for a Rare Disease

Suppose there is a large population and a disease that strikes a tiny proportion of the population. The tree diagram below summarizes information
about such a disease and about a medical test for it.

Overall, only 4 in 1000 of the population has the disease. The test is quite accurate: it has a very small false positive rate of 5 in 1000, and a
somewhat larger (though still small) false negative rate of 1 in 100.
Individuals might or might not know whether they have the disease; typically, people get tested to find out whether they have it.
So suppose a person is picked at random from the population and tested. If the test result is Positive, how would you classify them: Disease, or
No disease?
We can answer this by applying Bayes’ Rule and using our “more likely than not” classifier. Given that the person has tested Positive, the chance that
he or she has the disease is the proportion in the top branch, relative to the total proportion in the Test Positive branches.
(0.004 * 0.99)/(0.004 * 0.99 + 0.996*0.005 )

0.44295302013422816

Given that the person has tested Positive, the chance that he or she has the disease is about 44%. So we will classify them as: No disease.
This is a strange conclusion. We have a pretty accurate test, and a person who has tested Positive, and our classification is … that they don’t have
the disease? That doesn’t seem to make any sense.
When faced with a disturbing answer, the first thing to do is to check the calculations. The arithmetic above is correct. Let’s see if we can get the
same answer in a different way.
The function population returns a table of outcomes for 100,000 patients, with columns that show the True Condition and Test Result. The test is
the same as the one described in the tree. But the proportion who have the disease is an argument to the function.
We will call population with 0.004 as the argument, and then pivot to cross‑classify each of the 100,000 people.
population(0.004).pivot('Test Result', 'True Condition')

True Condition Negative Positive

Disease 4 396
No Disease 99102 498
The cells of the table have the right counts. For example, according to the description of the population, 4 in 1000 people have the disease. There are
100,000 people in the table, so 400 should have the disease. That’s what the table shows: 4 + 396 = 400. Of these 400, 99% get a Positive test
result: 0.99 x 400 = 396.
Among the Positives, the proportion that have the disease is:
396/(396 + 498)

0.4429530201342282

That’s the answer we got by using Bayes’ Rule. The counts in the Positives column show why it is less than 1/2. Among the Positives, more people
don’t have the disease than do have the disease.
The reason is that a huge fraction of the population doesn’t have the disease in the first place. The tiny fraction of those that falsely test Positive are
still greater in number than the people who correctly test Positive. This is easier to visualize in the tree diagram:

The proportion of true Positives is a large fraction (0.99) of a tiny fraction (0.004) of the population.
The proportion of false Positives is a tiny fraction (0.005) of a large fraction (0.996) of the population.
These two proportions are comparable; the second is a little larger.
So, given that the randomly chosen person tested positive, we were right to classify them as more likely than not to not have the disease.
18.2.2. A Subjective Prior
Being right isn’t always satisfying. Classifying a Positive patient as not having the disease still seems somehow wrong, for such an accurate test.
Since the calculations are right, let’s take a look at the basis of our probability calculation: the assumption of randomness.
Our assumption was that a randomly chosen person was tested and got a Positive result. But this doesn’t happen in reality. People go in to get tested
because they think they might have the disease, or because their doctor thinks they might have the disease. People getting tested are not
randomly chosen members of the population.
That is why our intuition about people getting tested was not fitting well with the answer that we got. We were imagining a realistic situation of a
patient going in to get tested because there was some reason for them to do so, whereas the calculation was based on a randomly chosen person
being tested.
So let’s redo our calculation under the more realistic assumption that the patient is getting tested because the doctor thinks there’s a chance the
patient has the disease.
Here it’s important to note that “the doctor thinks there’s a chance” means that the chance is the doctor’s opinion, not the proportion in the
population. It is called a subjective probability. In our context of whether or not the patient has the disease, it is also a subective prior probability.
Some researchers insist that all probabilities must be relative frequencies, but subjective probabilities abound. The chance that a candidate wins the
next election, the chance that a big earthquake will hit the Bay Area in the next decade, the chance that a particular country wins the next soccer
World Cup: none of these are based on relative frequencies or long run frequencies. Each one contains a subjective element. All calculations involving
them thus have a subjective element too.
Suppose the doctor’s subjective opinion is that there is a 5% chance that the patient has the disease. Then just the prior probabilities in the tree
diagram will change:

Given that the patient tests Positive, the chance that he or she has the disease is given by Bayes’ Rule.
(0.05 * 0.99)/(0.05 * 0.99 + 0.95 * 0.005)

0.9124423963133641

The effect of changing the prior is stunning. Even though the doctor has a pretty low prior probability (5%) that the patient has the disease, once the
patient tests Positive the posterior probability of having the disease shoots up to more than 91%.
If the patient tests Positive, it would be reasonable for the doctor to proceed as though the patient has the disease.

18.2.3. Confirming the Answer

Though the doctor’s opinion is subjective, we can generate an artificial population in which 5% of the people have the disease and are tested using
the same test. Then we can count people in different categories to see if the counts are consistent with the answer we got by using Bayes’ Rule.
We can use population(0.05) and pivot to construct the corresponding population and look at the counts in the four cells.
population(0.05).pivot('Test Result', 'True Condition')

True Condition Negative Positive

Disease 50 4950
No Disease 94525 475
In this artificially created population of 100,000 people, 5000 people (5%) have the disease, and 99% of them test Positive, leading to 4950 true
Positives. Compare this with 475 false Positives: among the Positives, the proportion that have the disease is the same as what we got by Bayes’
Rule.
4950/(4950 + 475)

0.9124423963133641

Because we can generate a population that has the right proportions, we can also use simulation to confirm that our answer is reasonable. The table
pop_05 contains a population of 100,000 people generated with the doctor’s prior disease probability of 5% and the error rates of the test. We take a
simple random sample of size 10,000 from the population, and extract the table positive consisting only of those in the sample that had Positive test
results.
pop_05 = population(0.05)

sample = pop_05.sample(10000, with_replacement=False)

positive = sample.where('Test Result', are.equal_to('Positive'))

Among these Positive results, what proportion were true Positives? That’s the proportion of Positives that had the disease:
positive.where('True Condition', are.equal_to('Disease')).num_rows/positive.num_rows

0.9218181818181819

Run the two cells a few times and you will see that the proportion of true Positives among the Positives hovers around the value of 0.912 that we
calculated by Bayes’ Rule.
You can also use the population function with a different argument to change the prior disease probability and see how the posterior probabilities
are affected.

By Ani Adhikari and John DeNero and David Wagner

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Data 8 Textbook

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Computational and Inferential Thinking: The Foundations of Data

1. What is Data Science?

1.1.1. Computational Tools

1.1.2. Statistical Techniques

1.3. Plotting the classics

# Display the chapters of Huckleberry Finn in a table.

1.3.1. Literary Characters

# Plot the cumulative counts:

cum_counts = counts.cumsum().with_column('Chapter', np.arange(1, 44, 1))

# Plot the cumulative counts.

cum_counts = counts.cumsum().with_column('Chapter', np.arange(1, 48, 1))

1.3.2. Another Kind of Character

Little Women Chapter Length Number of Periods

2. Causality and Experiments

2.2. Snow’s “Grand Experiment”

2.3. Establishing Causality

2.5. Terminology and Further Reading

File "<ipython-input-2-012ea60b41dd>", line 1

Exponentiation ** 2 ** 0.5 1.41421

A previously assigned name can be used in the expression to the right of =.

3.2.1. Example: Growth Rates

This same computation can be expressed using names and exponents.

3.3. Call Expressions

An equivalent expression could be expressed using the + and ** operators instead.

Return the logarithm of x to the given base.

3.4. Introduction to Tables

Flavor Color Price

Flavor Color Price

3.4.1. Choosing Sets of Columns

Flavor Color Price

3.4.2. Sorting Rows

Flavor Color Price

Flavor Color Price

3.4.3. Selecting Rows that Satisfy a Condition

Flavor Color Price

3.4.4. Example: Salaries in the NBA

PLAYER POSITION TEAM SALARY

PLAYER POSITION TEAM SALARY

PLAYER POSITION TEAM SALARY

PLAYER POSITION TEAM SALARY

This chapter will explore many useful types of data.

# Some float values

4.1.1. More About Float Values

"This won't work with a single-quoted string!"

Why not? Try it out.

4.2.1. String Methods

array([13.6 , 14.387, 14.585, 15.164])

Mean of Daily High Temperature

array(['noun', 'pronoun', 'verb', 'adverb', 'adjective', 'conjunction',

array([13.6 , 14.387, 14.585, 15.164])

array([56.48 , 57.8966, 58.253 , 59.2952])

5.1.1. Functions on Arrays

array([0.787, 0.198, 0.579])

array([ 3, 8, 13, 18, 23, 28])

array([ 1.5, 1. , 0.5, 0. , -0.5, -1. , -1.5])

5.2.1. Example: Leibniz’s formula for \(\pi\)

array([ 1, 5, 9, 13, 17])

array([ 1, 5, 9, ..., 9989, 9993, 9997])

The overall sum is

This is very close to \(\pi = 3.14159\dots\). Leibniz’s formula is looking good!

5.3. More on Arrays

array([13.6 , 14.387, 14.585, 15.164])

array([2.128, 2.371, 2.874, 3.728])

array([11.472, 12.016, 11.711, 11.436])

array([11.472, 12.016, 11.711, 11.436])

5.3.1. Elementwise arithmetic on pairs of numerical arrays

5.3.2. Example: Wallis’ Formula for \(\pi\)

Number of petals Name

Number of petals Name Color

Longitude Latitude City Direction Survivors

The Size of the Table

('Longitude', 'Latitude', 'City', 'Direction', 'Survivors')

Longitude Latitude City Direction Survivors

Longitude Latitude City Name Direction Survivors

Accessing the Data in a Column

array([145000, 140000, 127100, 100000, 55000, 24000, 20000, 12000])

Exponentiation 2 0.5 1.41421