Practical Statistics & Visualization With Python & Plotly

Practical Statistics & Visualization With Python & Plotly

Practical Statistics & Visualization With Python & Plotly

One day last week, I was googling “statistics with Python”, the results were somewhat unfruitful. Most literature, tutorials and articles focus on statistics with R, because R is a language dedicated to statistics and has more statistical analysis features than Python.

In two excellent statistics books, “Practical Statistics for Data Scientists” and “An Introduction to Statistical Learning”, the statistical concepts were all implemented in R.

Data science is a fusion of multiple disciplines, including statistics, computer science, information technology, and domain-specific fields. And we use powerful, open-source Python tools daily to manipulate, analyze, and visualize datasets.

And I would certainly recommend anyone interested in becoming a Data Scientist or Machine Learning Engineer to develop a deep understanding and practice constantly on statistical learning theories.

This prompts me to write a post for the subject. And I will use one dataset to review as many statistics concepts as I can and lets get started!

The Data

The data is the house prices data set that can be found here.

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
from plotly.offline import init_notebook_mode, iplot
import plotly.figure_factory as ff
import cufflinks
cufflinks.go_offline()
cufflinks.set_config_file(world_readable=True, theme='pearl')
import plotly.graph_objs as go
import plotly.plotly as py
import plotly
from plotly import tools
plotly.tools.set_credentials_file(username='XXX', api_key='XXX')
init_notebook_mode(connected=True)
pd.set_option('display.max_columns', 100)
df = pd.read_csv('house_train.csv')
df.drop('Id', axis=1, inplace=True)
df.head()

Univariate Data Analysis

Univariate analysis is perhaps the simplest form of statistical analysis, and the key fact is that only one variable is involved.

Describing Data

Statistical summary for numeric data include things like the mean, min, and max of the data, can be useful to get a feel for how large some of the variables are and what variables may be the most important.

df.describe().T

Statistical summary for categorical or string variables will show “count”, “unique”, “top”, and “freq”.

table_cat = ff.create_table(df.describe(include=['O']).T, index=True, index_title='Categorical columns')
iplot(table_cat)

Histogram

Plot a histogram of SalePrice of all the houses in the data.

df['SalePrice'].iplot(
    kind='hist',
    bins=100,
    xTitle='price',
    linecolor='black',
    yTitle='count',
    title='Histogram of Sale Price')

Boxplot

Plot a boxplot of SalePrice of all the houses in the data. Boxplots do not show the shape of the distribution, but they can give us a better idea about the center and spread of the distribution as well as any potential outliers that may exist. Boxplots and Histograms often complement each other and help us understand more about the data.

df['SalePrice'].iplot(kind='box', title='Box plot of SalePrice')
#### Histograms and Boxplots by Groups

Plotting by groups, we can see how a variable changes in response to another. For example, if there is a difference between house SalePrice with or with no central air conditioning. Or if house SalePrice varies according to the size of the garage, and so on.

Boxplot and histogram of house sale price grouped by with or with no air conditioning

trace0 = go.Box(
    y=df.loc[df['CentralAir'] == 'Y']['SalePrice'],
    name = 'With air conditioning',
    marker = dict(
        color = 'rgb(214, 12, 140)',
    )
)
trace1 = go.Box(
    y=df.loc[df['CentralAir'] == 'N']['SalePrice'],
    name = 'no air conditioning',
    marker = dict(
        color = 'rgb(0, 128, 128)',
    )
)
data = [trace0, trace1]
layout = go.Layout(
    title = "Boxplot of Sale Price by air conditioning"
)

fig = go.Figure(data=data,layout=layout)
py.iplot(fig)

boxplot_aircon.py

trace0 = go.Histogram(
    x=df.loc[df['CentralAir'] == 'Y']['SalePrice'], name='With Central air conditioning',
    opacity=0.75
)
trace1 = go.Histogram(
    x=df.loc[df['CentralAir'] == 'N']['SalePrice'], name='No Central air conditioning',
    opacity=0.75
)

data = [trace0, trace1]
layout = go.Layout(barmode='overlay', title='Histogram of House Sale Price for both with and with no Central air conditioning')
fig = go.Figure(data=data, layout=layout)

py.iplot(fig)

histogram_aircon.py

df.groupby('CentralAir')['SalePrice'].describe()

It is obviously that the mean and median sale price for houses with no air conditioning are much lower than the houses with air conditioning.

Boxplot and histogram of house sale price grouped by garage size

trace0 = go.Box(
    y=df.loc[df['GarageCars'] == 0]['SalePrice'],
    name = 'no garage',
    marker = dict(
        color = 'rgb(214, 12, 140)',
    )
)
trace1 = go.Box(
    y=df.loc[df['GarageCars'] == 1]['SalePrice'],
    name = '1-car garage',
    marker = dict(
        color = 'rgb(0, 128, 128)',
    )
)
trace2 = go.Box(
    y=df.loc[df['GarageCars'] == 2]['SalePrice'],
    name = '2-cars garage',
    marker = dict(
        color = 'rgb(12, 102, 14)',
    )
)
trace3 = go.Box(
    y=df.loc[df['GarageCars'] == 3]['SalePrice'],
    name = '3-cars garage',
    marker = dict(
        color = 'rgb(10, 0, 100)',
    )
)
trace4 = go.Box(
    y=df.loc[df['GarageCars'] == 4]['SalePrice'],
    name = '4-cars garage',
    marker = dict(
        color = 'rgb(100, 0, 10)',
    )
)
data = [trace0, trace1, trace2, trace3, trace4]
layout = go.Layout(
    title = "Boxplot of Sale Price by garage size"
)

fig = go.Figure(data=data,layout=layout)
py.iplot(fig)

boxplot_garage.py

The larger the garage, the higher house median price, this works until we reach 3-cars garage. Apparently, the houses with 3-cars garages have the highest median price, even higher than the houses with 4-cars garage.

Histogram of house sale price with no garage

df.loc[df['GarageCars'] == 0]['SalePrice'].iplot(
    kind='hist',
    bins=50,
    xTitle='price',
    linecolor='black',
    yTitle='count',
    title='Histogram of Sale Price of houses with no garage')

Histogram of house sale price with 1-car garage

df.loc[df['GarageCars'] == 1]['SalePrice'].iplot(
    kind='hist',
    bins=50,
    xTitle='price',
    linecolor='black',
    yTitle='count',
    title='Histogram of Sale Price of houses with 1-car garage')

Histogram of house sale price with 2-car garage

df.loc[df['GarageCars'] == 2]['SalePrice'].iplot(
    kind='hist',
    bins=100,
    xTitle='price',
    linecolor='black',
    yTitle='count',
    title='Histogram of Sale Price of houses with 2-car garage')

Histogram of house sale price with 3-car garage

df.loc[df['GarageCars'] == 3]['SalePrice'].iplot(
    kind='hist',
    bins=50,
    xTitle='price',
    linecolor='black',
    yTitle='count',
    title='Histogram of Sale Price of houses with 3-car garage')

Histogram of house sale price with 4-car garage

df.loc[df['GarageCars'] == 4]['SalePrice'].iplot(
    kind='hist',
    bins=10,
    xTitle='price',
    linecolor='black',
    yTitle='count',
    title='Histogram of Sale Price of houses with 4-car garage')

Frequency Table

Frequency tells us how often something happened. Frequency tables give us a snapshot of the data to allow us to find patterns.

Overall quality frequency table

x = df.OverallQual.value_counts()
x/x.sum()

Garage size frequency table

x = df.GarageCars.value_counts()
x/x.sum()

Central air conditioning frequency table

x = df.CentralAir.value_counts()
x/x.sum()

Numerical Summaries

A quick way to get a set of numerical summaries for a quantitative variable is to use the describe method.

df.SalePrice.describe()


We can also calculate individual summary statistics of SalePrice.

print("The mean of sale price, - Pandas method: ", df.SalePrice.mean())
print("The mean of sale price, - Numpy function: ", np.mean(df.SalePrice))
print("The median sale price: ", df.SalePrice.median())
print("50th percentile, same as the median: ", np.percentile(df.SalePrice, 50))
print("75th percentile: ", np.percentile(df.SalePrice, 75))
print("Pandas method for quantiles, equivalent to 75th percentile: ", df.SalePrice.quantile(0.75))

Calculate the proportion of the houses with sale price between 25th percentile (129975) and 75th percentile (214000).

print('The proportion of the houses with prices between 25th percentile and 75th percentile: ', np.mean((df.SalePrice >= 129975) & (df.SalePrice <= 214000)))

Calculate the proportion of the houses with total square feet of basement area between 25th percentile (795.75) and 75th percentile (1298.25).

print('The proportion of house with total square feet of basement area between 25th percentile and 75th percentile: ', np.mean((df.TotalBsmtSF >= 795.75) & (df.TotalBsmtSF <= 1298.25)))

Lastly, we calculate the proportion of the houses based on either conditions. Since some houses are under both criteria, the proportion below is less than the sum of the two proportions calculated above.

a = (df.SalePrice >= 129975) & (df.SalePrice <= 214000)
b = (df.TotalBsmtSF >= 795.75) & (df.TotalBsmtSF <= 1298.25)
print(np.mean(a | b))

Calculate sale price IQR for houses with no air conditioning.

q75, q25 = np.percentile(df.loc[df['CentralAir']=='N']['SalePrice'], [75,25])
iqr = q75 - q25
print('Sale price IQR for houses with no air conditioning: ', iqr)

Calculate sale price IQR for houses with air conditioning.

q75, q25 = np.percentile(df.loc[df['CentralAir']=='Y']['SalePrice'], [75,25])
iqr = q75 - q25
print('Sale price IQR for houses with air conditioning: ', iqr)

Stratification

Another way to get more information out of a dataset is to divide it into smaller, more uniform subsets, and analyze each of these “strata” on its own. We will create a new HouseAge column, then partition the data into HouseAge strata, and construct side-by-side boxplots of the sale price within each stratum.

df['HouseAge'] = 2019 - df['YearBuilt']
df["AgeGrp"] = pd.cut(df.HouseAge, [9, 20, 40, 60, 80, 100, 147]) # Create age strata based on these cut points
plt.figure(figsize=(12, 5)) 
sns.boxplot(x="AgeGrp", y="SalePrice", data=df);

The older the house, the lower the median price, that is, house price tends to decrease with age, until it reaches 100 years old. The median price of over 100 year old houses is higher than the median price of houses age between 80 and 100 years.

plt.figure(figsize=(12, 5))
sns.boxplot(x="AgeGrp", y="SalePrice", hue="CentralAir", data=df)
plt.show();

We have learned earlier that house price tends to differ between with and with no air conditioning. From above graph, we also find out that recent houses (9–40 years old) are all equipped with air conditioning.

plt.figure(figsize=(12, 5))
sns.boxplot(x="CentralAir", y="SalePrice", hue="AgeGrp", data=df)
plt.show();

We now group first by air conditioning, and then within air conditioning group by age bands. Each approach highlights a different aspect of the data.

We can also stratify jointly by House age and air conditioning to explore how building type varies by both of these factors simultaneously.

df1 = df.groupby(["AgeGrp", "CentralAir"])["BldgType"]
df1 = df1.value_counts()
df1 = df1.unstack()
df1 = df1.apply(lambda x: x/x.sum(), axis=1)
print(df1.to_string(float_format="%.3f"))

For all house age groups, vast majority type of dwelling in the data is 1Fam. The older the house, the more likely to have no air conditioning. However, for a 1Fam house over 100 years old, it is a little more likely to have air conditioning than not. There were neither very new nor very old duplex house types. For a 40–60 year old duplex house, it is more likely to have no air conditioning.

Multivariate Analysis

Multivariate analysis is based on the statistical principle of multivariate statistics, which involves observation and analysis of more than one statistical outcome variable at a time.

Scatter plot

A scatter plot is a very common and easily-understood visualization of quantitative bivariate data. Below we make a scatter plot of Sale Price against Above ground living area square feet. it is apparently a linear relationship.

df.iplot(
    x='GrLivArea',
    y='SalePrice',
    xTitle='Above ground living area square feet',
    yTitle='Sale price',
    mode='markers',
    title='Sale Price vs Above ground living area square feet')

2D Density Joint plot

The following two plot margins show the densities for the Sale Price and Above ground living area separately, while the plot in the center shows their density jointly.

trace1 = go.Scatter(
    x=df['GrLivArea'], y=df['SalePrice'], mode='markers', name='points',
    marker=dict(color='rgb(102,0,0)', size=2, opacity=0.4)
)
trace2 = go.Histogram2dContour(
    x=df['GrLivArea'], y=df['SalePrice'], name='density', ncontours=20,
    colorscale='Hot', reversescale=True, showscale=False
)
trace3 = go.Histogram(
    x=df['GrLivArea'], name='Ground Living area density',
    marker=dict(color='rgb(102,0,0)'),
    yaxis='y2'
)
trace4 = go.Histogram(
    y=df['SalePrice'], name='Sale Price density', marker=dict(color='rgb(102,0,0)'),
    xaxis='x2'
)
data = [trace1, trace2, trace3, trace4]

layout = go.Layout(
    showlegend=False,
    autosize=False,
    width=600,
    height=550,
    xaxis=dict(
        domain=[0, 0.85],
        showgrid=False,
        zeroline=False
    ),
    yaxis=dict(
        domain=[0, 0.85],
        showgrid=False,
        zeroline=False
    ),
    margin=dict(
        t=50
    ),
    hovermode='closest',
    bargap=0,
    xaxis2=dict(
        domain=[0.85, 1],
        showgrid=False,
        zeroline=False
    ),
    yaxis2=dict(
        domain=[0.85, 1],
        showgrid=False,
        zeroline=False
    )
)

fig = go.Figure(data=data, layout=layout)
py.iplot(fig)

price_GrLivArea.py

Heterogeneity and stratification

We continue exploring the relationship between SalePrice and GrLivArea, stratifying by BldgType.

trace0 = go.Scatter(x=df.loc[df['BldgType'] == '1Fam']['GrLivArea'], y=df.loc[df['BldgType'] == '1Fam']['SalePrice'], mode='markers', name='1Fam')
trace1 = go.Scatter(x=df.loc[df['BldgType'] == 'TwnhsE']['GrLivArea'], y=df.loc[df['BldgType'] == 'TwnhsE']['SalePrice'], mode='markers', name='TwnhsE')
trace2 = go.Scatter(x=df.loc[df['BldgType'] == 'Duplex']['GrLivArea'], y=df.loc[df['BldgType'] == 'Duplex']['SalePrice'], mode='markers', name='Duplex')
trace3 = go.Scatter(x=df.loc[df['BldgType'] == 'Twnhs']['GrLivArea'], y=df.loc[df['BldgType'] == 'Twnhs']['SalePrice'], mode='markers', name='Twnhs')
trace4 = go.Scatter(x=df.loc[df['BldgType'] == '2fmCon']['GrLivArea'], y=df.loc[df['BldgType'] == '2fmCon']['SalePrice'], mode='markers', name='2fmCon')

fig = tools.make_subplots(rows=2, cols=3)

fig.append_trace(trace0, 1, 1)
fig.append_trace(trace1, 1, 2)
fig.append_trace(trace2, 1, 3)
fig.append_trace(trace3, 2, 1)
fig.append_trace(trace4, 2, 2)

fig['layout'].update(height=400, width=800, title='Sale price Vs. Above ground living area square feet' +
                                                  ' by building type')
py.iplot(fig)

**stratify.py **

In almost all the building types, SalePrice and GrLivArea shows a positive linear relationship. In the results below, we see that the correlation between SalepPrice and GrLivArea in 1Fam building type is the highest at 0.74, while in Duplex building type the correlation is the lowest at 0.49.

print(df.loc[df.BldgType=="1Fam", ["GrLivArea", "SalePrice"]].corr())
print(df.loc[df.BldgType=="TwnhsE", ["GrLivArea", "SalePrice"]].corr())
print(df.loc[df.BldgType=='Duplex', ["GrLivArea", "SalePrice"]].corr())
print(df.loc[df.BldgType=="Twnhs", ["GrLivArea", "SalePrice"]].corr())
print(df.loc[df.BldgType=="2fmCon", ["GrLivArea", "SalePrice"]].corr())

Categorical bivariate analysis

We create a contingency table, counting the number of houses in each cell defined by a combination of building type and the general zoning classification.

x = pd.crosstab(df.MSZoning, df.BldgType)
x


Below we normalize within rows. This gives us the proportion of houses in each zoning classification that fall into each building type variable.

x.apply(lambda z: z/z.sum(), axis=1)

We can also normalize within the columns. This gives us the proportion of houses within each building type that fall into each zoning classification.

x.apply(lambda z: z/z.sum(), axis=0)

One step further, we will look at the proportion of houses in each zoning class, for each combination of the air conditioning and building type variables.

df.groupby(["CentralAir", "BldgType", "MSZoning"]).size().unstack().fillna(0).apply(lambda x: x/x.sum(), axis=1)

The highest proportion of houses in the data are the ones with zoning RL, with air conditioning and 1Fam building type. With no air conditioning, the highest proportion of houses are the ones in zoning RL and Duplex building type.

Mixed categorical and quantitative data

To get fancier, we are going to plot a violin plot to show the distribution of SalePrice for houses that are in each building type category.

data = []
for i in range(0,len(pd.unique(df['BldgType']))):
    trace = {
            "type": 'violin',
            "x": df['BldgType'][df['BldgType'] == pd.unique(df['BldgType'])[i]],
            "y": df['SalePrice'][df['BldgType'] == pd.unique(df['BldgType'])[i]],
            "name": pd.unique(df['BldgType'])[i],
            "box": {
                "visible": True
            },
            "meanline": {
                "visible": True
            }
        }
    data.append(trace)

        
fig = {
    "data": data,
    "layout" : {
        "title": "",
        "yaxis": {
            "zeroline": False,
        }
    }
}


py.iplot(fig)

price_violin_plot.py

We can see that the SalesPrice distribution of 1Fam building type are slightly right-skewed, and for the other building types, the SalePrice distributions are nearly normal.

Further reading:

Learn Python Through Exercises

The Python Bible™ | Everything You Need to Program in Python

The Ultimate Python Programming Tutorial

Python for Data Analysis and Visualization - 32 HD Hours !

Python Fundamentals

Data Science with Python explained

Data Science with Python explained

An overview of using Python for data science including Numpy, Scipy, pandas, Scikit-Learn, XGBoost, TensorFlow and Keras.

An overview of using Python for data science including Numpy, Scipy, pandas, Scikit-Learn, XGBoost, TensorFlow and Keras.

So you’ve heard of data science and you’ve heard of Python.

You want to explore both but have no idea where to start — data science is pretty complicated, after all.

Don’t worry — Python is one of the easiest programming languages to learn. And thanks to the hard work of thousands of open source contributors, you can do data science, too.

If you look at the contents of this article, you may think there’s a lot to master, but this article has been designed to gently increase the difficulty as we go along.

One article obviously can’t teach you everything you need to know about data science with python, but once you’ve followed along you’ll know exactly where to look to take the next steps in your data science journey.

Table contents:

  • Why Python?
  • Installing Python
  • Using Python for Data Science
  • Numeric computation in Python
  • Statistical analysis in Python
  • Data manipulation in Python
  • Working with databases in Python
  • Data engineering in Python
  • Big data engineering in Python
  • Further statistics in Python
  • Machine learning in Python
  • Deep learning in Python
  • Data science APIs in Python
  • Applications in Python
  • Summary
Why Python?

Python, as a language, has a lot of features that make it an excellent choice for data science projects.

It’s easy to learn, simple to install (in fact, if you use a Mac you probably already have it installed), and it has a lot of extensions that make it great for doing data science.

Just because Python is easy to learn doesn’t mean its a toy programming language — huge companies like Google use Python for their data science projects, too. They even contribute packages back to the community, so you can use the same tools in your projects!

You can use Python to do way more than just data science — you can write helpful scripts, build APIs, build websites, and much much more. Learning it for data science means you can easily pick up all these other things as well.

Things to note

There are a few important things to note about Python.

Right now, there are two versions of Python that are in common use. They are versions 2 and 3.

Most tutorials, and the rest of this article, will assume that you’re using the latest version of Python 3. It’s just good to be aware that sometimes you can come across books or articles that use Python 2.

The difference between the versions isn’t huge, but sometimes copying and pasting version 2 code when you’re running version 3 won’t work — you’ll have to do some light editing.

The second important thing to note is that Python really cares about whitespace (that’s spaces and return characters). If you put whitespace in the wrong place, your programme will very likely throw an error.

There are tools out there to help you avoid doing this, but with practice you’ll get the hang of it.

If you’ve come from programming in other languages, Python might feel like a bit of a relief: there’s no need to manage memory and the community is very supportive.

If Python is your first programming language you’ve made an excellent choice. I really hope you enjoy your time using it to build awesome things.

Installing Python

The best way to install Python for data science is to use the Anaconda distribution (you’ll notice a fair amount of snake-related words in the community).

It has everything you need to get started using Python for data science including a lot of the packages that we’ll be covering in the article.

If you click on Products -> Distribution and scroll down, you’ll see installers available for Mac, Windows and Linux.

Even if you have Python available on your Mac already, you should consider installing the Anaconda distribution as it makes installing other packages easier.

If you prefer to do things yourself, you can go to the official Python website and download an installer there.

Package Managers

Packages are pieces of Python code that aren’t a part of the language but are really helpful for doing certain tasks. We’ll be talking a lot about packages throughout this article so it’s important that we’re set up to use them.

Because the packages are just pieces of Python code, we could copy and paste the code and put it somewhere the Python interpreter (the thing that runs your code) can find it.

But that’s a hassle — it means that you’ll have to copy and paste stuff every time you start a new project or if the package gets updated.

To sidestep all of that, we’ll instead use a package manager.

If you chose to use the Anaconda distribution, congratulations — you already have a package manager installed. If you didn’t, I’d recommend installing pip.

No matter which one you choose, you’ll be able to use commands at the terminal (or command prompt) to install and update packages easily.

Using Python for Data Science

Now that you’ve got Python installed, you’re ready to start doing data science.

But how do you start?

Because Python caters to so many different requirements (web developers, data analysts, data scientists) there are lots of different ways to work with the language.

Python is an interpreted language which means that you don’t have to compile your code into an executable file, you can just pass text documents containing code to the interpreter!

Let’s take a quick look at the different ways you can interact with the Python interpreter.

In the terminal

If you open up the terminal (or command prompt) and type the word ‘python’, you’ll start a shell session. You can type any valid Python commands in there and they’d work just like you’d expect.

This can be a good way to quickly debug something but working in a terminal is difficult over the course of even a small project.

Using a text editor

If you write a series of Python commands in a text file and save it with a .py extension, you can navigate to the file using the terminal and, by typing python YOUR_FILE_NAME.py, can run the programme.

This is essentially the same as typing the commands one-by-one into the terminal, it’s just much easier to fix mistakes and change what your program does.

In an IDE

An IDE is a professional-grade piece of software that helps you manage software projects.

One of the benefits of an IDE is that you can use debugging features which tell you where you’ve made a mistake before you try to run your programme.

Some IDEs come with project templates (for specific tasks) that you can use to set your project out according to best practices.

Jupyter Notebooks

None of these ways are the best for doing data science with python — that particular honour belongs to Jupyter notebooks.

Jupyter notebooks give you the capability to run your code one ‘block’ at a time, meaning that you can see the output before you decide what to do next — that’s really crucial in data science projects where we often need to see charts before taking the next step.

If you’re using Anaconda, you’ll already have Jupyter lab installed. To start it you’ll just need to type ‘jupyter lab’ into the terminal.

If you’re using pip, you’ll have to install Jupyter lab with the command ‘python pip install jupyter’.

Numeric Computation in Python

It probably won’t surprise you to learn that data science is mostly about numbers.

The NumPy package includes lots of helpful functions for performing the kind of mathematical operations you’ll need to do data science work.

It comes installed as part of the Anaconda distribution, and installing it with pip is just as easy as installing Jupyter notebooks (‘pip install numpy’).

The most common mathematical operations we’ll need to do in data science are things like matrix multiplication, computing the dot product of vectors, changing the data types of arrays and creating the arrays in the first place!

Here’s how you can make a list into a NumPy array:

Here’s how you can do array multiplication and calculate dot products in NumPy:

And here’s how you can do matrix multiplication in NumPy:

Statistics in Python

With mathematics out of the way, we must move forward to statistics.

The Scipy package contains a module (a subsection of a package’s code) specifically for statistics.

You can import it (make its functions available in your programme) into your notebook using the command ‘from scipy import stats’.

This package contains everything you’ll need to calculate statistical measurements on your data, perform statistical tests, calculate correlations, summarise your data and investigate various probability distributions.

Here’s how to quickly access summary statistics (minimum, maximum, mean, variance, skew, and kurtosis) of an array using Scipy:

Data Manipulation with Python

Data scientists have to spend an unfortunate amount of time cleaning and wrangling data. Luckily, the Pandas package helps us do this with code rather than by hand.

The most common tasks that I use Pandas for are reading data from CSV files and databases.

It also has a powerful syntax for combining different datasets together (datasets are called DataFrames in Pandas) and performing data manipulation.

You can see the first few rows of a DataFrame using the .head method:

You can select just one column using square brackets:

And you can create new columns by combining others:

Working with Databases in Python

In order to use the pandas read_sql method, you’ll have to establish a connection to a database.

The most bulletproof method of connecting to a database is by using the SQLAlchemy package for Python.

Because SQL is a language of its own and connecting to a database depends on which database you’re using, I’ll leave you to read the documentation if you’re interested in learning more.

Data Engineering in Python

Sometimes we’d prefer to do some calculations on our data before they arrive in our projects as a Pandas DataFrame.

If you’re working with databases or scraping data from the web (and storing it somewhere), this process of moving data and transforming it is called ETL (Extract, transform, load).

You extract the data from one place, do some transformations to it (summarise the data by adding it up, finding the mean, changing data types, and so on) and then load it to a place where you can access it.

There’s a really cool tool called Airflow which is very good at helping you manage ETL workflows. Even better, it’s written in Python.

It was developed by Airbnb when they had to move incredible amounts of data around, you can find out more about it here.

Big Data Engineering in Python

Sometimes ETL processes can be really slow. If you have billions of rows of data (or if they’re a strange data type like text), you can recruit lots of different computers to work on the transformation separately and pull everything back together at the last second.

This architecture pattern is called MapReduce and it was made popular by Hadoop.

Nowadays, lots of people use Spark to do this kind of data transformation / retrieval work and there’s a Python interface to Spark called (surprise, surprise) PySpark.

Both the MapReduce architecture and Spark are very complex tools, so I’m not going to go into detail here. Just know that they exist and that if you find yourself dealing with a very slow ETL process, PySpark might help. Here’s a link to the official site.

Further Statistics in Python

We already know that we can run statistical tests, calculate descriptive statistics, p-values, and things like skew and kurtosis using the stats module from Scipy, but what else can Python do with statistics?

One particular package that I think you should know about is the lifelines package.

Using the lifelines package, you can calculate a variety of functions from a subfield of statistics called survival analysis.

Survival analysis has a lot of applications. I’ve used it to predict churn (when a customer will cancel a subscription) and when a retail store might be burglarised.

These are totally different to the applications the creators of the package imagined it would be used for (survival analysis is traditionally a medical statistics tool). But that just shows how many different ways there are to frame data science problems!

The documentation for the package is really good, check it out here.

Machine Learning in Python

Now this is a major topic — machine learning is taking the world by storm and is a crucial part of a data scientist’s work.

Simply put, machine learning is a set of techniques that allows a computer to map input data to output data. There are a few instances where this isn’t the case but they’re in the minority and it’s generally helpful to think of ML this way.

There are two really good machine learning packages for Python, let’s talk about them both.

Scikit-Learn

Most of the time you spend doing machine learning in Python will be spent using the Scikit-Learn package (sometimes abbreviated sklearn).

This package implements a whole heap of machine learning algorithms and exposes them all through a consistent syntax. This makes it really easy for data scientists to take full advantage of every algorithm.

The general framework for using Scikit-Learn goes something like this –

You split your dataset into train and test datasets:

Then you instantiate and train a model:

And then you use the metrics module to test how well your model works:

XGBoost

The second package that is commonly used for machine learning in Python is XGBoost.

Where Scikit-Learn implements a whole range of algorithms XGBoost only implements a single one — gradient boosted decision trees.

This package (and algorithm) has become very popular recently due to its success at Kaggle competitions (online data science competitions that anyone can participate in).

Training the model works in much the same way as a Scikit-Learn algorithm.

Deep Learning in Python

The machine learning algorithms available in Scikit-Learn are sufficient for nearly any problem. That being said, sometimes you need to use the most advanced thing available.

Deep neural networks have skyrocketed in popularity due to the fact that systems using them have outperformed nearly every other class of algorithm.

There’s a problem though — it’s very hard to say what a neural net is doing and why it’s making the decisions that it is. Because of this, their use in finance, medicine, the law and related professions isn’t widely endorsed.

The two major classes of neural network are convolutional neural networks (which are used to classify images and complete a host of other tasks in computer vision) and recurrent neural nets (which are used to understand and generate text).

Exploring how neural nets work is outside the scope of this article, but just know that the packages you’ll need to look for if you want to do this kind of work are TensorFlow (a Google contibution!) and Keras.

Keras is essentially a wrapper for TensorFlow that makes it easier to work with.

Data Science APIs in Python

Once you’ve trained a model, you’d like to be able to access predictions from it in other software. The way you do this is by creating an API.

An API allows your model to receive data one row at a time from an external source and return a prediction.

Because Python is a general purpose programming language that can also be used to create web services, it’s easy to use Python to serve your model via API.

If you need to build an API you should look into the pickle and Flask. Pickle allows you to save trained models on your hard-drive so that you can use them later. And Flask is the simplest way to create web services.

Web Applications in Python

Finally, if you’d like to build a full-featured web application around your data science project, you should use the Django framework.

Django is immensely popular in the web development community and was used to build the first version of Instagram and Pinterest (among many others).

Summary

And with that we’ve concluded our whirlwind tour of data science with Python.

We’ve covered everything you’d need to learn to become a full-fledged data scientist. If it still seems intimidating, you should know that nobody knows all of this stuff and that even the best of us still Google the basics from time to time.

Learn Data Science | How to Learn Data Science for Free

Learn Data Science | How to Learn Data Science for Free

Learn Data Science | How to Learn Data Science for Free. In this post, I have described a learning path and free online courses and tutorials that will enable you to learn data science for free.

The average cost of obtaining a masters degree at traditional bricks and mortar institutions will set you back anywhere between $30,000 and $120,000. Even online data science degree programs don’t come cheap costing a minimum of $9,000. So what do you do if you want to learn data science but can’t afford to pay this?

I trained into a career as a data scientist without taking any formal education in the subject. In this article, I am going to share with you my own personal curriculum for learning data science if you can’t or don’t want to pay thousands of dollars for more formal study.

The curriculum will consist of 3 main parts, technical skills, theory and practical experience. I will include links to free resources for every element of the learning path and will also be including some links to additional ‘low cost’ options. So if you want to spend a little money to accelerate your learning you can add these resources to the curriculum. I will include the estimated costs for each of these.

Technical skills

The first part of the curriculum will focus on technical skills. I recommend learning these first so that you can take a practical first approach rather than say learning the mathematical theory first. Python is by far the most widely used programming language used for data science. In the Kaggle Machine Learning and Data Science survey carried out in 2018 83% of respondents said that they used Python on a daily basis. I would, therefore, recommend focusing on this language but also spending a little time on other languages such as R.

Python Fundamentals

Before you can start to use Python for data science you need a basic grasp of the fundamentals behind the language. So you will want to take a Python introductory course. There are lots of free ones out there but I like the Codeacademy ones best as they include hands-on in-browser coding throughout.

I would suggest taking the introductory course to learn Python. This covers basic syntax, functions, control flow, loops, modules and classes.

Data analysis with python

Next, you will want to get a good understanding of using Python for data analysis. There are a number of good resources for this.

To start with I suggest taking at least the free parts of the data analyst learning path on dataquest.io. Dataquest offers complete learning paths for data analyst, data scientist and data engineer. Quite a lot of the content, particularly on the data analyst path is available for free. If you do have some money to put towards learning then I strongly suggest putting it towards paying for a few months of the premium subscription. I took this course and it provided a fantastic grounding in the fundamentals of data science. It took me 6 months to complete the data scientist path. The price varies from $24.50 to $49 per month depending on whether you pay annually or not. It is better value to purchase the annual subscription if you can afford it.

The Dataquest platform

Python for machine learning

If you have chosen to pay for the full data science course on Dataquest then you will have a good grasp of the fundamentals of machine learning with Python. If not then there are plenty of other free resources. I would focus to start with on scikit-learn which is by far the most commonly used Python library for machine learning.

When I was learning I was lucky enough to attend a two-day workshop run by Andreas Mueller one of the core developers of scikit-learn. He has however published all the material from this course, and others, on this Github repo. These consist of slides, course notes and notebooks that you can work through. I would definitely recommend working through this material.

Then I would suggest taking some of the tutorials in the scikit-learn documentation. After that, I would suggest building some practical machine learning applications and learning the theory behind how the models work — which I will cover a bit later on.

SQL

SQL is a vital skill to learn if you want to become a data scientist as one of the fundamental processes in data modelling is extracting data in the first place. This will more often than not involve running SQL queries against a database. Again if you haven’t opted to take the full Dataquest course then here are a few free resources to learn this skill.

Codeacamdemy has a free introduction to SQL course. Again this is very practical with in-browser coding all the way through. If you also want to learn about cloud-based database querying then Google Cloud BigQuery is very accessible. There is a free tier so you can try queries for free, an extensive range of public datasets to try and very good documentation.

Codeacademy SQL course

R

To be a well-rounded data scientist it is a good idea to diversify a little from just Python. I would, therefore, suggest also taking an introductory course in R. Codeacademy have an introductory course on their free plan. It is probably worth noting here that similar to Dataquest Codeacademy also offers a complete data science learning plan as part of their pro account (this costs from $31.99 to $15.99 per month depending on how many months you pay for up front). I personally found the Dataquest course to be much more comprehensive but this may work out a little cheaper if you are looking to follow a learning path on a single platform.

Software engineering

It is a good idea to get a grasp of software engineering skills and best practices. This will help your code to be more readable and extensible both for yourself and others. Additionally, when you start to put models into production you will need to be able to write good quality well-tested code and work with tools like version control.

There are two great free resources for this. Python like you mean it covers things like the PEP8 style guide, documentation and also covers object-oriented programming really well.

The scikit-learn contribution guidelines, although written to facilitate contributions to the library, actually cover the best practices really well. This covers topics such as Github, unit testing and debugging and is all written in the context of a data science application.

Deep learning

For a comprehensive introduction to deep learning, I don’t think that you can get any better than the totally free and totally ad-free fast.ai. This course includes an introduction to machine learning, practical deep learning, computational linear algebra and a code-first introduction to natural language processing. All their courses have a practical first approach and I highly recommend them.

Fast.ai platform

Theory

Whilst you are learning the technical elements of the curriculum you will encounter some of the theory behind the code you are implementing. I recommend that you learn the theoretical elements alongside the practical. The way that I do this is that I learn the code to be able to implement a technique, let’s take KMeans as an example, once I have something working I will then look deeper into concepts such as inertia. Again the scikit-learn documentation contains all the mathematical concepts behind the algorithms.

In this section, I will introduce the key foundational elements of theory that you should learn alongside the more practical elements.

The khan academy covers almost all the concepts I have listed below for free. You can tailor the subjects you would like to study when you sign up and you then have a nice tailored curriculum for this part of the learning path. Checking all of the boxes below will give you an overview of most elements I have listed below.

Maths

Calculus

Calculus is defined by Wikipedia as “the mathematical study of continuous change.” In other words calculus can find patterns between functions, for example, in the case of derivatives, it can help you to understand how a function changes over time.

Many machine learning algorithms utilise calculus to optimise the performance of models. If you have studied even a little machine learning you will probably have heard of Gradient descent. This functions by iteratively adjusting the parameter values of a model to find the optimum values to minimise the cost function. Gradient descent is a good example of how calculus is used in machine learning.

What you need to know:

Derivatives

  • Geometric definition
  • Calculating the derivative of a function
  • Nonlinear functions

Chain rule

  • Composite functions
  • Composite function derivatives
  • Multiple functions

Gradients

  • Partial derivatives
  • Directional derivatives
  • Integrals

Linear Algebra

Many popular machine learning methods, including XGBOOST, use matrices to store inputs and process data. Matrices alongside vector spaces and linear equations form the mathematical branch known as Linear Algebra. In order to understand how many machine learning methods work it is essential to get a good understanding of this field.

What you need to learn:

Vectors and spaces

  • Vectors
  • Linear combinations
  • Linear dependence and independence
  • Vector dot and cross products

Matrix transformations

  • Functions and linear transformations
  • Matrix multiplication
  • Inverse functions
  • Transpose of a matrix

Statistics

Here is a list of the key concepts you need to know:

Descriptive/Summary statistics

  • How to summarise a sample of data
  • Different types of distributions
  • Skewness, kurtosis, central tendency (e.g. mean, median, mode)
  • Measures of dependence, and relationships between variables such as correlation and covariance

Experiment design

  • Hypothesis testing
  • Sampling
  • Significance tests
  • Randomness
  • Probability
  • Confidence intervals and two-sample inference

Machine learning

  • Inference about slope
  • Linear and non-linear regression
  • Classification

Practical experience

The third section of the curriculum is all about practice. In order to truly master the concepts above you will need to use the skills in some projects that ideally closely resemble a real-world application. By doing this you will encounter problems to work through such as missing and erroneous data and develop a deep level of expertise in the subject. In this last section, I will list some good places you can get this practical experience from for free.

“With deliberate practice, however, the goal is not just to reach your potential but to build it, to make things possible that were not possible before. This requires challenging homeostasis — getting out of your comfort zone — and forcing your brain or your body to adapt.”, Anders Ericsson, Peak: Secrets from the New Science of Expertise

Kaggle, et al

Machine learning competitions are a good place to get practice with building machine learning models. They give access to a wide range of data sets, each with a specific problem to solve and have a leaderboard. The leaderboard is a good way to benchmark how good your knowledge at developing a good model actually is and where you may need to improve further.

In addition to Kaggle, there are other platforms for machine learning competitions including Analytics Vidhya and DrivenData.

Driven data competitions page

UCI Machine Learning Repository

The UCI machine learning repository is a large source of publically available data sets. You can use these data sets to put together your own data projects this could include data analysis and machine learning models, you could even try building a deployed model with a web front end. It is a good idea to store your projects somewhere publically such as Github as this can create a portfolio showcasing your skills to use for future job applications.


UCI repository

Contributions to open source

One other option to consider is contributing to open source projects. There are many Python libraries that rely on the community to maintain them and there are often hackathons held at meetups and conferences where even beginners can join in. Attending one of these events would certainly give you some practical experience and an environment where you can learn from others whilst giving something back at the same time. Numfocus is a good example of a project like this.

In this post, I have described a learning path and free online courses and tutorials that will enable you to learn data science for free. Showcasing what you are able to do in the form of a portfolio is a great tool for future job applications in lieu of formal qualifications and certificates. I really believe that education should be accessible to everyone and, certainly, for data science at least, the internet provides that opportunity. In addition to the resources listed here, I have previously published a recommended reading list for learning data science available here. These are also all freely available online and are a great way to complement the more practical resources covered above.

Thanks for reading!

Python For Data Analysis | Build a Data Analysis Library from Scratch | Learn Python in 2019

Python For Data Analysis - Build a Data Analysis Library from Scratch - Learn Python in 2019

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Immerse yourself in a long, comprehensive project that teaches advanced Python concepts to build an entire library

You’ll learn

  • How to build a Python library similar pandas
  • How to complete a large, comprehensive project
  • Test-driven development with pytest
  • Environment creation
  • Advanced Python topics such as special methods and property decorators
  • A fully-functioning library that you can use to data analysis