comp20008-project01/parta1.py

import pandas as pd
import argparse

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

# filter out data past 2020
all_covid_data = all_covid_data[(all_covid_data['date'] >= '2020-01-01') & (all_covid_data['date'] <= '2020-12-31')]
all_covid_data.date = pd.to_datetime(all_covid_data.date)

# create groupby objects and sum new cases/deaths by month
new_cases = all_covid_data.loc[:, ['location', 'date', 'new_cases']]
new_cases_grouped = new_cases.groupby([new_cases.date.dt.month, new_cases.location]).new_cases.sum()

new_deaths = all_covid_data.loc[:, ['location', 'date', 'new_deaths']]
new_deaths_grouped = new_deaths.groupby([new_deaths.date.dt.month, new_deaths.location]).new_deaths.sum()

# convert multi-indexed series to dataframe
new_cases_grouped = new_cases_grouped.to_frame()
new_cases_grouped = pd.DataFrame(new_cases_grouped.to_records())
new_deaths_grouped = new_deaths_grouped.to_frame()
new_deaths_grouped = pd.DataFrame(new_deaths_grouped.to_records())

# sort by location, then date
new_cases_grouped.sort_values(by = ['location', 'date'], inplace = True)
new_deaths_grouped.sort_values(by = ['location', 'date'], inplace = True)

# merge new_deaths and new_cases
aggregated_data = new_cases_grouped.merge(new_deaths_grouped, how = 'outer', left_on = ['location', 'date'], right_on = ['location', 'date'])

# filter out all entries that aren't at the end of the month
all_covid_data['end_of_month'] = pd.to_datetime(all_covid_data['date']).dt.is_month_end
all_covid_data = all_covid_data.loc[all_covid_data.end_of_month, :]

# extract monthly total cases and total deaths
total_cases = all_covid_data.loc[:, ['location', 'date', 'total_cases']]
total_cases.date = total_cases.date.dt.month

total_deaths = all_covid_data.loc[:, ['location', 'date', 'total_deaths']]
total_deaths.date = total_deaths.date.dt.month

# merge total_deaths and total_cases into aggregated_data
aggregated_data = aggregated_data.merge(total_cases, how = 'outer', left_on = ['location', 'date'], right_on = ['location', 'date'])
aggregated_data = aggregated_data.merge(total_deaths, how = 'outer', left_on = ['location', 'date'], right_on = ['location', 'date'])
aggregated_data.rename(columns = {'date': 'month'}, inplace = True)

# compute case fatality rate for each month
aggregated_data['case_fatality_rate'] = (aggregated_data['new_deaths'] / aggregated_data['new_cases'])
aggregated_data = aggregated_data.reindex(columns = ['location', 'month', 'case_fatality_rate', 'total_cases', 'new_cases', 'total_deaths', 'new_deaths'])

# output results to csv and stdout
print(aggregated_data.head(5))
aggregated_data.to_csv('owid-covid-data-2020-monthly.csv')