comp20008-project01/parta2.py

import pandas as pd
import argparse
import matplotlib.pyplot as plt
import numpy as np

# parse input arguments
parser = argparse.ArgumentParser()
parser.add_argument('scatter_a', help = 'output path of figure 1')
parser.add_argument('scatter_b', help = 'output path of figure 2')
args = parser.parse_args()

all_covid_data = pd.read_csv('data/owid-covid-data.csv', \
    encoding = 'ISO-8859-1')

# filter out data - only need 2020-12-31
all_covid_data = all_covid_data[(all_covid_data['date'] == '2020-12-31')]
all_covid_data.date = pd.to_datetime(all_covid_data.date)

# extract total cases and deaths for 2020 per country
total_cases = all_covid_data.loc[:, ['location', 'total_cases']]
total_cases.set_index(['location'], inplace = True)
total_deaths = all_covid_data.loc[:, ['location', 'total_deaths']]

# merge total_cases and total_deaths
aggregated_data = total_cases.merge(total_deaths, how = 'inner', \
    on = 'location')

# compute case fatality rate for each country
aggregated_data['case_fatality_rate'] = \
    (aggregated_data['total_deaths'] / aggregated_data['total_cases'])

# extract case fatality rate from aggregated data
case_fatality_rate = aggregated_data.loc[:, ['case_fatality_rate']]

# plot case-fatality-rate against number of cases
# this excludes some locations as they are outliers
plt.scatter(total_cases, case_fatality_rate)
plt.xlim(0, 3000000)
plt.ylim(0, 0.075)
plt.ylabel('Case fatality rate')
plt.xlabel('Total confirmed cases in 2020')
plt.grid(True)
plt.savefig(args.scatter_a, dpi = 250.0)

# plot case-fatality-rate against the log of the number of cases
total_cases = total_cases.apply(np.log10, axis = 1)
plt.scatter(total_cases, case_fatality_rate)
plt.xlim(0, 9)
plt.xlabel('Log of total confirmed cases in 2020')
plt.savefig(args.scatter_b, dpi = 250.0)