Analyze Covid Vaccination Progress Using Python

This article was published as a part of the Data Science Blogathon

Introduction

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Dataset

                                                                          Image Source

IMPORT LIBRARIES 

For analyzing data, we need some libraries. In this section, we are importing all the required libraries like pandas, NumPy, matplotlib, plotly, seaborn, and word cloud that are required for data analysis. Check the below code to import all the required libraries.

import pandas as pd
import numpy as np
import matplotlib.pyplot as plt
import plotly.express as px
import plotly.graph_objects as go
import matplotlib.patches as mpatches
from plotly.subplots import make_subplots
from wordcloud import WordCloud
import seaborn as sns  
sns.set(color_codes = True)
sns.set(style="whitegrid")
import plotly.figure_factory as ff
from plotly.colors import n_colors

READ DATA AND BASIC INFORMATION 

Read the CSV file using pandas read_csv() function and show the output using head() function.

info() function is used to get the overview of data like data type of feature, a number of null values in each column, and many more.

df.info()

Observation:

The above picture shows that there are many null values in our dataset. We will deal with these null values later in this blog. There are two data types as seen from the table object means string and float.

The below function is used to get the total count of null values in each feature.

df.isnull().sum()

Observation:
The below picture shows tables like country, date, vaccines, source_name has 0 null values. Features like people_fully_vaccinated have a maximum of 2866 null values.

DATA CLEANING 

Dataset has many null values as we have seen before. To get rid of it we need to clean the data first, After cleaning we will perform our further analysis. For cleaning the dataset we will perform many steps. Some of these steps are shown below

df.fillna(value = 0, inplace = True)
df.total_vaccinations = df.total_vaccinations.astype(int)
df.people_vaccinated = df.people_vaccinated.astype(int)
df.people_fully_vaccinated = df.people_fully_vaccinated.astype(int)
df.daily_vaccinations_raw = df.daily_vaccinations_raw.astype(int)
df.daily_vaccinations = df.daily_vaccinations.astype(int)
df.total_vaccinations_per_hundred = df.total_vaccinations_per_hundred.astype(int)
df.people_fully_vaccinated_per_hundred = df.people_fully_vaccinated_per_hundred.astype(int)
df.daily_vaccinations_per_million = df.daily_vaccinations_per_million.astype(int)
df.people_vaccinated_per_hundred = df.people_vaccinated_per_hundred.astype(int)
date = df.date.str.split('-', expand =True)
date

df['year'] = date[0]
df['month'] = date[1]
df['day'] = date[2]
df.year = pd.to_numeric(df.year)
df.month = pd.to_numeric(df.month)
df.day = pd.to_numeric(df.day)
df.date = pd.to_datetime(df.date)
df.head()

SOME FEATURES 

Let’s get some details about our features using the below code

print('Data point starts from ',df.date.min(),'n')
print('Data point ends at ',df.date.max(),'n')
print('Total no of countries in the data set ',len(df.country.unique()),'n')
print('Total no of unique vaccines in the data set ',len(df.vaccines.unique()),'n')

df.info()

DATA VISUALIZATION 

In this section, we are going to draw some visuals to get insights from our dataset. So let’s started.

df.describe()

df.country.unique()

def size(m,n):
    fig = plt.gcf();
    fig.set_size_inches(m,n);

Word Art of Countries

wordCloud = WordCloud(
    background_color='white',
    max_font_size = 50).generate(' '.join(df.country))
plt.figure(figsize=(15,7))
plt.axis('off')
plt.imshow(wordCloud)
plt.show()

Total Vaccinated Till Date 

In this section, we are going to see how many total vaccines have been used in each country. Check the below code for more information. The data shows the United States has administrated most vaccines in the world followed by China, United Kingdom, England, India and at the last some countries includes Saint Helena, San Marino has 0 vaccination.

country_wise_total_vaccinated = {}
for country in df.country.unique() : 
    vaccinated = 0
    for i in range(len(df)) : 
        if df.country[i] == country : 
            vaccinated += df.daily_vaccinations[i]
    country_wise_total_vaccinated[country] = vaccinated 
#     made a seperate dict from the df 
    country_wise_total_vaccinated_df = pd.DataFrame.from_dict(country_wise_total_vaccinated,
                                                         orient='index',
                                                         columns = ['total_vaccinted_till_date'])
#     converted dict to df 
country_wise_total_vaccinated_df.sort_values(by = 'total_vaccinted_till_date', ascending = False, inplace = True)
country_wise_total_vaccinated_df

fig = px.bar(country_wise_total_vaccinated_df, 
             y = 'total_vaccinted_till_date',
             x = country_wise_total_vaccinated_df.index,
             color = 'total_vaccinted_till_date',
             color_discrete_sequence= px.colors.sequential.Viridis_r
            )
fig.update_layout(
    title={
            'text' : "Vaccination till date in various countries",
            'y':0.95,
            'x':0.5
        },
    xaxis_title="Countries",
    yaxis_title="Total vaccinated",
    legend_title="Total vaccinated"
)
fig.show()

Country Wise Daily Vaccination 

To check what is the vaccination trend in each country, check the below code. We are drawing the line plot where the x-axis is the date and the y-axis is the count of daily vaccination, Colours Is set to be the country.

fig = px.line(df, x = 'date', y ='daily_vaccinations', color = 'country')
fig.update_layout(
    title={
            'text' : "Daily vaccination trend",
            'y':0.95,
            'x':0.5
        },
    xaxis_title="Date",
    yaxis_title="Daily Vaccinations"
)
fig.show()

Observation:

There is a mixed kind of trend among each country. Sometimes a particular country shows a positive trend and sometimes it shows a negative trend.

Plot Till Date Function

# helper function
def plot_till_date(value1, value2, title, color1, color2) : 
    so_far_dict = {}
    for dates in df.date.unique() : 
        so_far_dict[dates], value1_count, value2_count = [], 0, 0
        for i in range(len(df)) : 
            if df.date[i] == dates : 
                value1_count += df[value1][i]
                value2_count += df[value2][i]
#         if dates not in so_far_dict.keys() : 
        so_far_dict[dates].append(value1_count) 
        so_far_dict[dates].append(value2_count)
    so_far_df = pd.DataFrame.from_dict(so_far_dict, orient = 'index', columns=[value1, value2])
    so_far_df.reset_index(inplace = True)
#     return so_far_df
    so_far_df.sort_values(by='index', inplace = True)
    plot = go.Figure(data=[go.Scatter( 
            x = so_far_df['index'], 
            y = so_far_df[value1], 
            stackgroup='one', 
            name = value1, 
            marker_color= color1), 
                           go.Scatter( 
            x = so_far_df['index'], 
            y = so_far_df[value2], 
            stackgroup='one',
            name = value2, 
            marker_color= color2) 
        ]) 
    plot.update_layout(
    title={
            'text' : title,
            'y':0.95,
            'x':0.5
        },
        xaxis_title="Date"
    )
    return plot.show()

People vaccinated vs people fully vaccinated in the world : 

In this section, let’s analyze how many people vaccinated vs the people which are fully vaccinated in the world. We are drawing a kind of curve where the x-axis is Date and the y-axis is the count of people that are fully vaccinated in the world

plot_till_date('people_fully_vaccinated', 'people_vaccinated','People vaccinated vs Fully vaccinated till date', '#c4eb28', '#35eb28')

The People vaccinated vs people fully vaccinated per hundred in the world 

In this section, let’s analyze how many people vaccinated vs the people which are fully vaccinated in the world per hundred. We are drawing a kind of curve where the x-axis is Date and the y-axis is the count of people that are fully vaccinated in the world per hundred

plot_till_date('people_fully_vaccinated_per_hundred', 'people_vaccinated_per_hundred', 'People vaccinated vs Fully vaccinated per hundred till date', '#0938e3','#7127cc')

Observation

• People fully vaccinated in the world per hundred is around 2
• People that are vaccinated in the world is around 7

Pie-Plot 

In this section, we are going to draw pip-plots. For more details check the below code:

def plot_pie(value, title, color) : 
    new_dict = {}
    for v in df[value].unique() : 
        value_count = 0
        for i in range(len(df)) : 
            if df[value][i] == v : 
                value_count += 1 
        new_dict[v] = value_count 
#     print(new_dict)
    new_df = pd.DataFrame.from_dict(new_dict, orient = 'index', columns = ['Total'])
    if color == 'plasma' : 
        fig = px.pie(new_df, values= 'Total',
                     names = new_df.index,
                     title = title,
                     color_discrete_sequence=px.colors.sequential.Plasma)
    elif color == 'rainbow' : 
        fig = px.pie(new_df, values= 'Total',
                     names = new_df.index,
                     title = title,
                     color_discrete_sequence=px.colors.sequential.Rainbow)
    else :
        fig = px.pie(new_df, values= 'Total',
                     names = new_df.index,
                     title = title)
    fig.update_layout(
        title={
            'y':0.95,
            'x':0.5
        },
        legend_title = value
    )
    return fig.show()
    plot_pie('vaccines', 'Various vaccines and their uses', 'plasma')

Most Used Vaccine 

Let’s see what all vaccines are used in the different part of the world:

df.vaccines.unique()

Word art of Vaccines 

Word Cloud is a unique way to get information from our dataset. The words are shown in the form of art where the size proportional depends on how much the particular word repeated in the dataset. This is made by using the WordCloud library. Check the below code on how to draw word cloud

wordCloud = WordCloud(
    background_color='white',
    max_font_size = 50).generate(' '.join(df.vaccines))
plt.figure(figsize=(12,5))
plt.axis('off')
plt.imshow(wordCloud)
plt.show()

Daily vaccination trend per million  

In this section, we will what is the trend of vaccination per million. We are going to draw a line plot where the x-axis is Date and the y-axis is daily vaccination per million. Check the below code for more information:

fig = px.line(df, x = 'date', y ='daily_vaccinations_per_million', color = 'country')
fig.update_layout(
    title=
            'text' : "Daily vaccination trend per million",
            'y':0.95,
            'x':0.5
        },
    xaxis_title="Date",
    yaxis_title="Daily Vaccinations per million"
)
fig.show()

Observation

• Seychelles and Israel has the highest number of vaccinations per million
• On 10th Jan Gibraltar has the highest vaccination per million

Total vaccinated – India vs the USA  

In this section, we will see what is the trend of vaccination among two great countries India and the USA. We are going to draw a line plot where the x-axis is Date and the y-axis is daily vaccination. Check the below code for more information:

india_usa = [df[df.country == 'United States'], df[df.country == 'India']]
result = pd.concat(india_usa)
fig = px.line(result, x = 'date', y ='total_vaccinations', color = 'country')
fig.update_layout(
    title={
            'text' : "Total vaccinated - India vs USA",
            'y':0.95,
            'x':0.5
        },
    xaxis_title="Date",
    yaxis_title="Total Vaccinations"
)
fig.show()

Observation

• The USA has started vaccination drive very early
• India is moving quite steadily despite it has started vaccination late.

MAPS 

In this section, we are going to see how vaccinations are going in different countries using maps. The colour signifies how many people have been vaccinated. Check the below maps for more details.

Most vaccinated country

plot_map('total_vaccinations','Most vaccinated country', None)

Vaccines Used in Different countries

plot_map('vaccines','Vaccines Used in Different countries', None)

People fully vaccinated in Different countries 

plot_map('people_fully_vaccinated','People fully vaccinated in Different countries', 'haline')

Key Observations:

Akshay Gupta 31 Aug 2022