COVID-19 Growth By State (US)

#hide

%matplotlib inline

import requests

import pandas as pd

import numpy as np

import matplotlib.pyplot as plt

from matplotlib.ticker import ScalarFormatter

states_url = "https://covidtracking.com/api/states/daily"

us_url = "https://covidtracking.com/api/us/daily"

case_threshold = 100

#hide

r = requests.get(states_url)

states_df = pd.DataFrame(r.json())

states_df['date'] = pd.to_datetime(states_df.date, format="%Y%m%d")

states_df = states_df[['date', 'state', 'positive']].sort_values('date')

cols = {}

for state in states_df.state.unique():

    cases = states_df[(states_df.state == state) & (states_df.positive > 100)]

    cases = cases.reset_index().positive.reset_index(drop=True)

    if len(cases):

        cols[state] = cases

r = requests.get(us_url)

us_df = pd.DataFrame(r.json())

us_df['date'] = pd.to_datetime(us_df.date, format="%Y%m%d")

us_df = us_df[['date', 'positive']].sort_values('date')

cols['US'] = us_df.positive.reset_index(drop=True)

#collapse-hide

fig = plt.figure(figsize=(13.4, 9.54))

ax = plt.axes()

pd.concat(cols, axis=1).plot(ax=ax, marker='o')

plt.title('COVID19 Growth in US as a whole and by state')

plt.ylabel('Cumulative confirmed cases')

plt.xlabel(f'Number of days since {case_threshold}th case')

plt.annotate('Based on COVID Data Repository by the COVID Tracking Project\n'

             f'Latest data from {states_df.date.max().strftime("%Y-%m-%d")}, varies by state\n'

             'Chart by Avy Faingezicht, @avyfain', 

             (0.07, 0.02), xycoords='figure fraction', fontsize=10);

plt.legend(loc="lower right")

x = np.linspace(0, plt.xlim()[1])

plt.plot(x, 100 * (1.33) ** x, ls='--', color='k', label='33% daily growth')

plt.annotate('33% Daily Growth', 

             (0.85, 0.75), xycoords='figure fraction', fontsize=10);

formatter = ScalarFormatter()

formatter.set_scientific(False)

ax.yaxis.set_major_formatter(formatter)

ax.yaxis.set_minor_formatter(formatter)

#collapse-hide

fig = plt.figure(figsize=(13.4, 9.54))

ax = plt.axes()

pd.concat(cols, axis=1).plot(ax=ax, marker='o', logy=True)

plt.title('COVID19 Growth in US as a whole and by state')

plt.ylabel('Cumulative confirmed cases (log scale)')

plt.xlabel(f'Number of days since {case_threshold}th case')

plt.annotate('Based on COVID Data Repository by The COVID Tracking Project\n'

             f'Latest data from {states_df.date.max().strftime("%Y-%m-%d")}, varies by state\n'

             'Chart by Avy Faingezicht, @avyfain', 

             (0.07, 0.02), xycoords='figure fraction', fontsize=10);

plt.legend(loc="lower right")

plt.plot(x, 100 * (1.33) ** x, ls='--', color='k', label='33% daily growth')

plt.annotate('33% Daily Growth', 

             (0.85, 0.75), xycoords='figure fraction', fontsize=10);

ax.yaxis.set_major_formatter(formatter)

ax.yaxis.set_minor_formatter(formatter)