Modules, packages, and EDA in Python

Time for data!

The data analysis process

Exploratory data analysis

• “Detective work” to summarize and explore datasets

Includes:

• Data acquisition and input
• Data cleaning and wrangling (“tidying”)
• Data transformation and summarization
• Data visualization

Your core Python tools for EDA: NumPy, pandas, and seaborn/matplotlib

Modules and packages

• Module: file containing variables, functions, etc. that can be imported into a Python session with the import statement
• Package: directory of modules that perform similar tasks (e.g. data visualization, statistics, etc.)
• Thousands upon thousands of Python packages available - that do just about anything!

Built-in packages

• Many packages are included in stdlib, the standard library that ships with Python
• Popular modules: re for regular expressions; os for operating system functions; random for random-number generation; and many more. Full list: https://docs.python.org/3/library/

The PyData ecosystem

NumPy

• Extension to Python; the core Python package for numerical computing
• Standard import: import numpy as np
• Data structure: the NumPy array. Sort of like a list - but with more methods, and can be multidimensional

import numpy as np

y = np.array([[2, 4, 6, 8, 10, 12], 
             [1, 3, 5, 7, 9, 11], 
             [10, 12, 14, 18, 22, 14], 
             [9, 3, 3, 3, 3, 1]])
            

Pandas

• Built on top of NumPy; adds support for table-like data structures in Python
• Standard import: import pandas as pd
• Sequences of data are stored as Series objects, which collectively form DataFrames

import pandas as pd

df = pd.DataFrame(y, columns = ['x' + str(num) for num in range(1, 7)])

The pandas DataFrame

• Commonly, DataFrames are created by reading in external data, like CSV files
• Download link: https://github.com/walkerke/geog30323/blob/main/data/colleges.csv (click Download raw file)

# To read in CSV files, we use the pd.read_csv function 
colleges = pd.read_csv("colleges.csv")

Tutorial: working with external data in Colab

• Download colleges.csv from the link to your computer
• In Colab, click the folder icon in the left sidebar to open the Files pane, then the upload button, and choose the file
• It lands in /content, Colab’s working directory - so pd.read_csv("colleges.csv") finds it
• Uploaded files disappear when the runtime disconnects. Re-upload, or mount your Google Drive

The pandas DataFrame

• Each observation forms a row, defined by an index; attributes of those observations are found in the columns of the DataFrame
• Columns are accessible as indices, e.g. colleges['median_earn'], or as attributes of the data frame, e.g. colleges.median_earn

The Python namespace

• When you declare variables, define functions, import modules, etc., you are adding objects to the Python namespace
• To remove objects from the Python namespace, use the del statement

Imports and the namespace

• Imported modules can be referenced in multiple ways:

# All of these are equivalent

import pandas
pandas.read_csv("colleges.csv")

import pandas as pd
pd.read_csv("colleges.csv")

from pandas import *
read_csv("colleges.csv")

Levels of measurement

• Nominal: qualitative, descriptive, categories
• Ordinal: ordering or ranking; however, no information about distance between ranks
• Interval: additive; the zero is arbitrary (0°F is not “no temperature”)
• Ratio: multiplicative; natural zero (zero means an absence of a value)

Make sure you know your column types (dtypes) and levels of measurement before doing analysis!

Measures of central tendency

• Mode: the most typical value in a distribution
• Median: the “balancing point” in a distribution (50 percent of observations above and below)
• Mean: the arithmetic average of a distribution

The mean of a sample (\(\overline{x}\)) is calculated as follows:

\[\overline{x} = \dfrac{x_1 + x_2 + ... + x_n}{n}\]

where \(n\) is the number of elements in the sample.

Measures of dispersion

• Range: difference between maximum and minimum values in a distribution
• Interquartile range: difference between the values at the 25 percent and 75 percent points in a distribution
• Variance and standard deviation

Standard deviation

• Computed as the square root of the variance; denoted by \(\sigma\).
  
• Offers a standardized way to discuss the spread of a distribution. For example, in a normally distributed sample:
  • About 68 percent of the values will be within one standard deviation of the mean
  • About 95 percent of the values will be within two standard deviations of the mean
  • About 99.7 percent of the values will be within three standard deviations of the mean

Descriptive statistics in pandas

• Descriptive stats are available in pandas as data frame methods, e.g. colleges.mean(), colleges.std()
• Calling .describe() will give you back a number of important descriptive stats at once

.describe()

colleges.describe()

Exploratory visualization

• Often, when exploring a dataset, you’ll want to use graphical representations of your data to help reveal insights/trends
• Visualization: Graphical representation of data

Visualization in Python

• Core visualization package in Python: matplotlib
• seaborn: extension to matplotlib to make your graphics look nicer! Standard import: import seaborn as sns.

Histograms

• Histogram: graphical representation of a frequency distribution
• Observations are organized into bins, and plotted with values along the x-axis and the number of observations in each bin along the y-axis
• Normal distribution: histogram is approximately symmetrical (a “bell curve”)
• Histograms are built into pandas

Before you plot: what shape do you expect?

Example histogram (pandas method)

import seaborn as sns
sns.set_style("darkgrid")

colleges.median_earn.hist()

Example histogram (seaborn function)

# Try the `bins` argument to modify the plot appearance
sns.histplot(data = colleges, x = "median_earn")

Density plots

• Smooth representations of your data can be produced with kernel density plots
• Accessible from both pandas and seaborn

sns.kdeplot(data = colleges, x = "median_earn", fill = True)

Box plots

• Also termed “box and whisker plots” - alternative way to show distribution of values graphically

sns.boxplot(data = colleges, y = "median_earn", color = "green")

Anatomy of a box plot

• Dots beyond the whiskers: outliers

Violin plots

• Combinations of box plots and kernel density plots

sns.violinplot(data = colleges, x = "median_earn", color = "cyan")