Some COVID-19 graphs

growth.py

"""
Usage:

wget https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv
python growth.py
"""

import csv
from datetime import date

import matplotlib.pyplot as plt


LOCKDOWN = {
	('Hubei', 'China'):   date(2020, 1, 23),
	('', 'Italy'):        date(2020, 3, 11),
	('', 'France'):       date(2020, 3, 17),
}

COLORS = {
	('Hubei', 'China'):   's-r',
	('', 'Italy'):        '^-b',
	('', 'France'):       'o-c',
}


def get_start_index(my_date):
	start = date(2020, 1, 22)
	return (my_date - start).days + 4


growth = []

with open('time_series_covid19_confirmed_global.csv') as _:
	reader = csv.reader(_)
	next(reader)  # Header
	for row in reader:
		key = (row[0], row[1])
		lockdown = LOCKDOWN.get(key)
		if lockdown is None:
			continue
		start_index = get_start_index(lockdown) - 1
		series = [int(cases) for cases in row[start_index:] if cases != '']
		# Removing duplicated counts
		for i, cases in enumerate(series[1:]):
			if cases == series[i] and i < 30:
				series[i+1] = (series[i] + series[i+2]) // 2
		growth.append((
			key,
			[
				(series[n] - series[n-1])/series[n-1]*100
				for n in range(1, len(series))
			]
		))


graph = plt.figure().subplots()
graph.set_title("Growth of Covid-19 cases starting from lockdown")
graph.set_xlabel("Days since lockdown")
graph.set_ylabel("New cases (as percentage of cumulative cases)")
graph.axis([1, 40, 0, 60])
graph.grid(True, color=(0.9, 0.9, 0.9, 1))

for key, series in growth:
	graph.plot(
		[i+1 for i in range(len(series))],
		series,
		COLORS[key],
	)

graph.legend([', '.join([stuff for stuff in key if stuff]) for key, _ in growth])

plt.savefig('growth.svg')
plt.show()

recovery.py

"""
Usage:

wget https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv
wget https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv
python recovery.py
"""

import csv

import matplotlib.pyplot as plt


start_col = 37  # Febrary 24

data = {}
with open('time_series_covid19_confirmed_global.csv') as confirmed, \
     open('time_series_covid19_recovered_global.csv') as recovered:
    for label, fileobj in zip(['confirmed', 'recovered'], [confirmed, recovered]):
        reader = csv.reader(fileobj)
        for row in reader:
            if row[:2] == ['Hubei', 'China']:
                data[label] = [int(c) for c in row[start_col:] if c != '']
                break


graph = plt.figure().subplots()
graph.set_title("Unrecovered cases vs all confirmed cases in Hubei after "
                "30 days of lockdown")
graph.set_xlabel("Days since second month of lockdown")
graph.set_ylabel("Number of unrecovered and confirmed cases")

confirmed = data['confirmed']
patients = [c - r for c, r in zip(data['confirmed'], data['recovered'])]
graph.bar(range(len(confirmed)), confirmed)
graph.bar(range(len(patients)), patients)

graph.legend(['Confirmed', 'Unrecovered'])

plt.savefig('recovery.svg')
plt.show()