covid_data.py

import pandas as pd
import pylab as plt

df_allcauses = pd.read_excel('datasetfinalcorrected3.xlsx', sheet_name='Table 2', header=4, nrows=38)
df_covid = pd.read_excel('datasetfinalcorrected3.xlsx', sheet_name='Table 1', header=4, nrows=38)


for k in df_covid.keys():
    if k.startswith('Age-st'):
        df_covid[k] = pd.to_numeric(df_covid[k], errors='coerce').fillna(0)
        df_allcauses[k] =pd.to_numeric( df_allcauses[k], errors='coerce').fillna(0)
        
        

assert (df_covid['Week number'] == df_allcauses['Week number']).all()


plt.plot(df_allcauses['Week number'], df_allcauses['Age-standardised mortality rate per 100,000'], label='Unvaccinated')
plt.plot(df_allcauses['Week number'], df_allcauses['Age-standardised mortality rate per 100,000.3'], label='Fully vaccinated')
plt.legend()
plt.xlabel('Week number')
plt.title('Age-standardised mortality rate per 100,000 in England, 2021')


plt.figure()
plt.plot(df_covid['Week number'], df_allcauses['Age-standardised mortality rate per 100,000'] - df_covid['Age-standardised mortality rate per 100,000'], label='Unvaccinated')
plt.plot(df_covid['Week number'], df_allcauses['Age-standardised mortality rate per 100,000.3'] - df_covid['Age-standardised mortality rate per 100,000.3'], label='Fully vaccinated')
plt.legend()
plt.xlabel('Week number')
plt.title('COVID-excluded Age-standardised mortality rate per 100,000 in England, 2021')

plt.figure()
plt.plot(df_covid['Week number'],  df_covid['Age-standardised mortality rate per 100,000'], label='Unvaccinated')
plt.plot(df_covid['Week number'], df_covid['Age-standardised mortality rate per 100,000.3'], label='Fully vaccinated')
plt.legend()
plt.xlabel('Week number')
plt.title('COVID age-standardised mortality rate per 100,000 in England, 2021')
plt.show()