Showing posts with label data science. Show all posts
Showing posts with label data science. Show all posts

# The summary is not the whole picture

If you just use summary statistics to describe your data, you can miss the bigger picture, sometimes literally so. In this blog post, I'm going to show you how relying on summaries alone can lead you catastrophically astray and I'm going to tell you how you can avoid making career-damaging mistakes.

The datasaurus is why you need to visualize your data. Source: Alberto Cairo. Open source.

# What are summary statistics?

Summary statistics are parameters like the mean, standard deviation, and correlation coefficient; they summarize the properties of the data and the relationship between variables. For example, if the correlation coefficient, r, is about 0.8 for two data sets x and y, we might think there's a relationship between them, but if it's about 0, we might think there isn't.

The use of summary statistics is widely taught, every textbook emphasizes them, and almost everyone uses them. But if you use summary statistics in isolation from other methods you might miss important relationships - you should always visualize your data as we'll see.

# Anscombe's Quartet

Take a look at the four plots below. They're obviously quite different, but they all have the same summary statistics!

Here are the summary statistics data:

PropertyValue
Mean of x9
Sample variance of x : ${\displaystyle \sigma ^{2}}$11
Mean of y7.50
Sample variance of y : ${\displaystyle \sigma ^{2}}$4.125
Correlation between x and y0.816
Linear regression liney = 3.00 + 0.500x
Coefficient of determination of the linear regression : ${\displaystyle R^{2}}$0.67

These plots were developed in 1973 by the statistician Francis Anscombe to make exactly this point: you can't rely on summary statistics, you need to visualize your data. The graphical relationship between the x and y variables is different in each case and implies different things. By plotting the data out, we can see what the relationships are, but summary statistics hide what's going on.

# The datasaurus

Let's zoom forward to 2016. The justly famous Alberto Cairo tweeted about Anscombe's quartet and illustrated the point with this cool set of summary statistics. He later expanded on his tweet in a short blog post.

Property Value
n 142
mean 54.2633
x standard deviation 16.7651
y mean 47.8323
y standard deviation 26.9353
Pearson correlation -0.0645

What might you conclude from these summary statistics? I might say, the correlation coefficient is close to zero so there's not much of a relationship between the x and the y variables. I might conclude there's no interesting relationship between the x and y variables - but I would be wrong.

The summary might not mean anything to you, but the visualization surely will. This is the datasaurus data set, the x and the y variables draw out a dinosaur.

# The datasaurus dozen

Two researchers at Autodesk Research took things a stage further. They started with Alberto Cairo's datasaurus and created a dozen other charts with exactly the same summary statistics as the datasaurus. Here they all are.

The summary statistics look like noise, but the charts reveal the underlying relationships between the x and y variables. Some of these relationships are obviously fun, like the star, but there are others that imply more meaningful relationships.

If all this sounds a bit abstract, let's think about how this might manifest itself in business. Let's imagine you're an analyst working for a large company. You have data on sales by store size for Europe and you've been asked to analyze the data to gain insights. You're under time pressure, so you fire up a Python notebook and get some quick summary statistics. You get summary statistics that look like the ones I showed you above. So you conclude there's nothing interesting in the data, but you might be very wrong.

You should plot the data out and look at the chart. You might see something that looks like the slanting charts above, maybe something like this:

the individual diagonal lines might correspond to different European countries (different regulations, different planning rules, different competition, etc.). There could be a very significant relationship that you would have missed by relying on summary data.

(The Autodesk Research team have posted their work as a paper you can read here.)

# Lessons learned

The lessons you should take away from all this are simple:

• summary statistics hide a lot
• there are many relationships between variables that will give summary statistics that look like noise
• always visualize your data!

## Tuesday, March 24, 2020

### John Snow, cholera, and the origins of data science

The John Snow story is so well known, it borders on the cliched, but I discovered some twists and turns I hadn't known that shed new light on what happened and on how to interpret Snow's results. Snow's story isn't just a foundational story for epidemiology, it's a foundational story for data science too.

(Image credit: Cholera bacteria, CDC; Broad Street pump, Betsy Weber; John Snow, Wikipedia)

To very briefly summarize: John Snow was a nineteenth-century doctor with an interest in epidemiology and cholera. When cholera hit London in 1854, he played a pivotal role in understanding cholera in two quite different ways, both of which are early examples of data science practices.

The first way was his use of registry data recording the number of cholera deaths by London district. Snow was able to link the prevalence of deaths to the water company that supplied water to each district. The Southwark & Vauxhall water company sourced their water from a relatively polluted part of the river Thames, while the Lambeth water company took their water from a relatively unpolluted part of the Thames. As it turned out, there was a clear relationship between drinking water source and cholera deaths, with polluted water leading to more deaths.

This wasn't a randomized control trial, but was instead an early form of difference-in-difference analysis. Difference-in-difference analysis was popularized by Card and Krueger in the mid-1990's and is now widely used in econometrics and other disciplines. Notably, there are many difference-in-difference tutorials that use Snow's data set to teach the method.

I've reproduced one of Snow's key tables below, the most important piece is the summary at the bottom comparing deaths from cholera by water supply company. You can see the attraction of this dataset for data scientists, it's calling out for the use of groupby.

The second way is a more dramatic tale and guaranteed his continuing fame. In 1854, there was an outbreak of cholera in the Golden Square part of Soho in London. Right from the start, Snow suspected the water pump at Broad Street was the source of the infection. Snow conducted door-to-door inquiries, asking what people ate and drank. He was able to establish that people who drank water from the pump died at a much higher rate than those that did not. The authorities were desperate to stop the infection, and despite the controversial nature of Snow's work, they listened and took action; famously, they removed the pump handle and the cholera outbreak stopped.

Snow continued his analysis after the pump handle was removed and wrote up his results (along with the district study I mentioned above) in a book published in 1855. In the second edition of his book, he included his famous map, which became an iconic data visualization for data science.

Snow knew where the water pumps were and knew where deaths had occurred. He merged this data into a map-bar chart combination; he started with a street map of the Soho area and placed a bar for each death that occurred at an address. His map showed a concentration of deaths near the Broad Street pump.

I've reproduced a section of his map below. The Broad Street pump I've highlighted in red and you can see a high concentration of deaths nearby. There are two properties that suffered few deaths despite being near the pump, the workhouse and the brewery. I've highlighted the workhouse in green. Despite housing a large number of people, few died. The workhouse had its own water supply, entirely separate from the Broad Street pump. The brewery (highlighted in yellow) had no deaths either; they supplied their workers with free beer (made from boiled water).

(Source: adapted from Wikipedia)

I've been fascinated with this story for a while now, and recent events caused me to take a closer look. There's a tremendous amount of this story that I've left out, including:

• The cholera bacteria and the history of cholera infections.
• The state of medical knowledge at the time and how the prevailing theory blocked progress on preventing and treating cholera.
• The intellectual backlash against John Snow.
• The 21st century controversy surrounding the John Snow pub.

I've written up the full story in a longer article you can get from my website. Here's a link to my longer article.