Chapter - 4

Exploratory Data Analysis

using Python

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 Overview of Python Libraries for Data
Tutorial Content Scientists

Reading Data; Selecting and Filtering the Data; Data manipulation,

sorting, grouping, rearranging

Plotting the data

Descriptive statistics

Inferential statistics

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Python Libraries for Data Science
Many popular Python toolboxes/libraries:
• NumPy
• SciPy All these libraries are
• Pandas installed on the SCC
• SciKit-Learn

Visualization libraries
• matplotlib
• Seaborn

and many more …

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Python Libraries for Data Science
NumPy:
 introduces objects for multidimensional arrays and matrices, as well as
functions that allow to easily perform advanced mathematical and statistical
operations on those objects

 provides vectorization of mathematical operations on arrays and matrices

which significantly improves the performance

 many other python libraries are built on NumPy

Link: http://www.numpy.org/

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Python Libraries for Data Science
SciPy:
 collection of algorithms for linear algebra, differential equations, numerical
integration, optimization, statistics and more

 part of SciPy Stack

 built on NumPy

Link: https://www.scipy.org/scipylib/

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Python Libraries for Data Science
Pandas:
 adds data structures and tools designed to work with table-like data (similar
to Series and Data Frames in R)

 provides tools for data manipulation: reshaping, merging, sorting, slicing,

aggregation etc.

 allows handling missing data

Link: http://pandas.pydata.org/

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Python Libraries for Data Science
SciKit-Learn:
 provides machine learning algorithms: classification, regression, clustering,
model validation etc.

 built on NumPy, SciPy and matplotlib

Link: http://scikit-learn.org/

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Python Libraries for Data Science
matplotlib:
 python 2D plotting library which produces publication quality figures in a
variety of hardcopy formats

 a set of functionalities similar to those of MATLAB

 line plots, scatter plots, barcharts, histograms, pie charts etc.

 relatively low-level; some effort needed to create advanced visualization

Link: https://matplotlib.org/

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Python Libraries for Data Science
Seaborn:
 based on matplotlib

 provides high level interface for drawing attractive statistical graphics

 Similar (in style) to the popular ggplot2 library in R

Link: https://seaborn.pydata.org/

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Login to the Shared Computing
Cluster
• Use your SCC login information if you have SCC account

• If you are using tutorial accounts see info on the blackboard

Note: Your password will not be displayed while you enter it.

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Selecting Python Version on the SCC
# view available python versions on the SCC
[scc1 ~] module avail python

# load python 3 version

[scc1 ~] module load python/3.6.2

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Download tutorial notebook
# On the Shared Computing Cluster
[scc1 ~] cp /project/scv/examples/python/data_analysis/dataScience.ipynb .

# On a local computer save the link:

http://rcs.bu.edu/examples/python/data_analysis/dataScience.ipynb

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Start Jupyter nootebook
# On the Shared Computing Cluster
[scc1 ~] jupyter notebook

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Loading Python Libraries
In [ ]: #Import Python Libraries
import numpy as np
import scipy as sp
import pandas as pd
import matplotlib as mpl
import seaborn as sns

Press Shift+Enter to execute the jupyter cell

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 Reading data using pandas
In [ ]: #Read csv file
df = pd.read_csv("http://rcs.bu.edu/examples/python/data_analysis/Salaries.csv")

Note: The above command has many optional arguments to fine-tune the data import process.

There is a number of pandas commands to read other data formats:

pd.read_excel('myfile.xlsx',sheet_name='Sheet1', index_col=None,
na_values=['NA'])
pd.read_stata('myfile.dta')
pd.read_sas('myfile.sas7bdat')
pd.read_hdf('myfile.h5','df')
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 Exploring data frames
In [3]: #List first 5 records
df.head()

Out[3]:

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 Hands-on exercises

 Try to read the first 10, 20, 50 records;

 Can you guess how to view the last few records; Hint:

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Data Frame data types
Pandas Type Native Python Type Description
object string The most general dtype. Will be
assigned to your column if column
has mixed types (numbers and
strings).

int64 int Numeric characters. 64 refers to

the memory allocated to hold this
character.

float64 float Numeric characters with decimals.

If a column contains numbers and
NaNs(see below), pandas will
default to float64, in case your
missing value has a decimal.

datetime64, timedelta[ns] N/A (but see the datetime module Values meant to hold time data.
in Python’s standard library) Look into these for time series
experiments.

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 Data Frame data types
In [4]: #Check a particular column type
df['salary'].dtype

Out[4]: dtype('int64')

In [5]: #Check types for all the columns

df.dtypes

Out[4]: rank object

discipline object
phd int64
service int64
sex object
salary int64
dtype: object
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Data Frames attributes
Python objects have attributes and methods.

df.attribute description
dtypes list the types of the columns
columns list the column names
axes list the row labels and column names
ndim number of dimensions

size number of elements

shape return a tuple representing the dimensionality
values numpy representation of the data

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 Hands-on exercises

 Find how many records this data frame has;

 How many elements are there?

 What are the column names?

 What types of columns we have in this data frame?

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Data Frames methods
Unlike attributes, python methods have parenthesis.
All attributes and methods can be listed with a dir() function: dir(df)

df.method() description
head( [n] ), tail( [n] ) first/last n rows

describe() generate descriptive statistics (for numeric columns only)

max(), min() return max/min values for all numeric columns

mean(), median() return mean/median values for all numeric columns

std() standard deviation

sample([n]) returns a random sample of the data frame

dropna() drop all the records with missing values

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 Hands-on exercises

 Give the summary for the numeric columns in the dataset

 Calculate standard deviation for all numeric columns;

 What are the mean values of the first 50 records in the dataset? Hint: use

head() method to subset the first 50 records and then calculate the mean

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Selecting a column in a Data Frame
Method 1: Subset the data frame using column name:
df['sex']

Method 2: Use the column name as an attribute:

df.sex

Note: there is an attribute rank for pandas data frames, so to select a column with a name
"rank" we should use method 1.

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 Hands-on exercises

 Calculate the basic statistics for the salary column;

 Find how many values in the salary column (use count method);

 Calculate the average salary;

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 Data Frames groupby method
Using "group by" method we can:
• Split the data into groups based on some criteria
• Calculate statistics (or apply a function) to each group
• Similar to dplyr() function in R
In [ ]: #Group data using rank
df_rank = df.groupby(['rank'])

In [ ]: #Calculate mean value for each numeric column per each group
df_rank.mean()

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 Data Frames groupby method

Once groupby object is create we can calculate various statistics for each group:
In [ ]: #Calculate mean salary for each professor rank:
df.groupby('rank')[['salary']].mean()

Note: If single brackets are used to specify the column (e.g. salary), then the output is Pandas Series object.
When double brackets are used the output is a Data Frame
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 Data Frames groupby method

groupby performance notes:

- no grouping/splitting occurs until it's needed. Creating the groupby object
only verifies that you have passed a valid mapping
- by default the group keys are sorted during the groupby operation. You may
want to pass sort=False for potential speedup:

In [ ]: #Calculate mean salary for each professor rank:

df.groupby(['rank'], sort=False)[['salary']].mean()

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 Data Frame: filtering

To subset the data we can apply Boolean indexing. This indexing is commonly
known as a filter. For example if we want to subset the rows in which the salary
value is greater than $120K:
In [ ]: #Calculate mean salary for each professor rank:
df_sub = df[ df['salary'] > 120000 ]

Any Boolean operator can be used to subset the data:

> greater; >= greater or equal;
< less; <= less or equal;
== equal; != not equal;
In [ ]: #Select only those rows that contain female professors:
df_f = df[ df['sex'] == 'Female' ]
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Data Frames: Slicing

There are a number of ways to subset the Data Frame:

• one or more columns
• one or more rows
• a subset of rows and columns

Rows and columns can be selected by their position or label

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 Data Frames: Slicing

When selecting one column, it is possible to use single set of brackets, but the
resulting object will be a Series (not a DataFrame):
In [ ]: #Select column salary:
df['salary']

When we need to select more than one column and/or make the output to be a
DataFrame, we should use double brackets:
In [ ]: #Select column salary:
df[['rank','salary']]

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 Data Frames: Selecting rows

If we need to select a range of rows, we can specify the range using ":"

In [ ]: #Select rows by their position:

df[10:20]

Notice that the first row has a position 0, and the last value in the range is omitted:
So for 0:10 range the first 10 rows are returned with the positions starting with 0
and ending with 9

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 Data Frames: method loc

If we need to select a range of rows, using their labels we can use method loc:

In [ ]: #Select rows by their labels:

df_sub.loc[10:20,['rank','sex','salary']]

Out[ ]:

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 Data Frames: method iloc

If we need to select a range of rows and/or columns, using their positions we can
use method iloc:
In [ ]: #Select rows by their labels:
df_sub.iloc[10:20,[0, 3, 4, 5]]

Out[ ]:

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Data Frames: method iloc
(summary)
df.iloc[0] # First row of a data frame
df.iloc[i] #(i+1)th row
df.iloc[-1] # Last row

df.iloc[:, 0] # First column

df.iloc[:, -1] # Last column

df.iloc[0:7] #First 7 rows

df.iloc[:, 0:2] #First 2 columns
df.iloc[1:3, 0:2] #Second through third rows and first 2 columns
df.iloc[[0,5], [1,3]] #1st and 6th rows and 2nd and 4th columns

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 Data Frames: Sorting

We can sort the data by a value in the column. By default the sorting will occur in
ascending order and a new data frame is return.

In [ ]: # Create a new data frame from the original sorted by the column Salary
df_sorted = df.sort_values( by ='service')
df_sorted.head()

Out[ ]:

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 Data Frames: Sorting

We can sort the data using 2 or more columns:

In [ ]: df_sorted = df.sort_values( by =['service', 'salary'], ascending = [True, False])
df_sorted.head(10)

Out[ ]:

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 Missing Values
Missing values are marked as NaN
In [ ]: # Read a dataset with missing values
flights = pd.read_csv("http://rcs.bu.edu/examples/python/data_analysis/flights.csv")

In [ ]: # Select the rows that have at least one missing value

flights[flights.isnull().any(axis=1)].head()

Out[ ]:

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Missing Values
There are a number of methods to deal with missing values in the data frame:
df.method() description
dropna() Drop missing observations

dropna(how='all') Drop observations where all cells is NA

dropna(axis=1, how='all') Drop column if all the values are missing

dropna(thresh = 5) Drop rows that contain less than 5 non-missing values

fillna(0) Replace missing values with zeros

isnull() returns True if the value is missing

notnull() Returns True for non-missing values

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Missing Values
• When summing the data, missing values will be treated as zero
• If all values are missing, the sum will be equal to NaN
• cumsum() and cumprod() methods ignore missing values but preserve them in
the resulting arrays
• Missing values in GroupBy method are excluded (just like in R)
• Many descriptive statistics methods have skipna option to control if missing
data should be excluded . This value is set to True by default (unlike R)

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Aggregation Functions in Pandas
Aggregation - computing a summary statistic about each group, i.e.
• compute group sums or means
• compute group sizes/counts

Common aggregation functions:

min, max
count, sum, prod
mean, median, mode, mad
std, var

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 Aggregation Functions in Pandas
agg() method are useful when multiple statistics are computed per column:
In [ ]: flights[['dep_delay','arr_delay']].agg(['min','mean','max'])

Out[ ]:

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Basic Descriptive Statistics
df.method() description
describe Basic statistics (count, mean, std, min, quantiles, max)

min, max Minimum and maximum values

mean, median, mode Arithmetic average, median and mode

var, std Variance and standard deviation

sem Standard error of mean

skew Sample skewness

kurt kurtosis

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 Graphics to explore the data
Seaborn package is built on matplotlib but provides high level
interface for drawing attractive statistical graphics, similar to ggplot2
library in R. It specifically targets statistical data visualization

To show graphs within Python notebook include inline directive:

In [ ]: %matplotlib inline

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Graphics
description
distplot histogram
barplot estimate of central tendency for a numeric variable
violinplot similar to boxplot, also shows the probability density of the
data
jointplot Scatterplot
regplot Regression plot
pairplot Pairplot
boxplot boxplot
swarmplot categorical scatterplot
factorplot General categorical plot

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Basic statistical Analysis
statsmodel and scikit-learn - both have a number of function for statistical analysis

The first one is mostly used for regular analysis using R style formulas, while scikit-learn is
more tailored for Machine Learning.

statsmodels:
• linear regressions
• ANOVA tests
• hypothesis testings
• many more ...

scikit-learn:
• kmeans
• support vector machines
• random forests
• many more ...

See examples in the Tutorial Notebook

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