/
data.py
376 lines (363 loc) · 11.3 KB
/
data.py
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import pandas as pd
import numpy as np
import json
import os
import time
def jhu_data(remote=True):
"""Fetch data from JHU set on Github and partially parse it.
Inputs:
- remote: if True, pull files from Github. Otherwise, use local copies.
Outputs:
- cases_df: # of confirmed cases (pandas dataframe)
- deaths_df: # of confirmed deaths (pandas dataframe)
- data_dates: full range of dates of data (human-readable format)
"""
if remote:
url = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv"
else:
url = "/Users/ketch/Research/Projects/covid-data-sources/JHU_data/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
# Check that file has been updated today
timestamp = os.path.getmtime(url)
if (time.time()-timestamp)/3600 > 12:
print('Warning: data file is more than 12 hours old. Please update.')
cases_df = pd.read_csv(url)
# No more recovered data:
# url = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Recovered.csv"
#recovered = pd.read_csv(url)
if remote:
url = "https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
else:
url = "/Users/ketch/Research/Projects/COVID-19/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv"
deaths_df = pd.read_csv(url)
today = cases_df.columns[-1]
data_dates = pd.date_range(start='1/22/20',end=today)
return cases_df, deaths_df, data_dates
def load_time_series(region):
"""
Fetch data and parse to get time series of confirmed cases and deaths.
For now, only works with JHU data.
"""
cases_df, deaths_df, data_dates = jhu_data()
#if region in US_state_population.keys():
# postal_code = us_state_abbrev[region]
# state_str = postal_code+', USA'
# with open('/Users/ketch/Downloads/timeseries-byLocation.json') as file:
# state_data = json.load(file)
# for date in data_dates:
# print(date, state_data[state_str]['dates'][date.strftime('%Y-%-m-%-d')].keys())
# cum_deaths = [state_data[state_str]['dates'][date.strftime('%Y-%-m-%-d')]['deaths_df'] for date in data_dates]
# cum_cases = [state_data[state_str]['dates'][date.strftime('%Y-%-m-%-d')]['cases_df'] for date in data_dates]
#
#else:
rows = cases_df['Country/Region'].isin([region])
cum_cases = [cases_df[day.strftime('%-m/%-d/%y')][rows].sum() for day in data_dates]
if not np.any(rows==True):
raise(Exception)
rows = deaths_df['Country/Region'].isin([region])
cum_deaths = [deaths_df[day.strftime('%-m/%-d/%y')][rows].sum() for day in data_dates]
return data_dates, np.array(cum_cases), np.array(cum_deaths)
population_smallset = {
'Austria': 8.822e6,
'France': 66.99e6,
'Germany': 82.79e6,
'Korea, South': 51.47e6,
'Italy' : 60.48e6,
'Netherlands': 17.18e6,
'Spain' : 46.66e6,
'Switzerland': 8.57e6,
'United Kingdom': 66.44e6,
'US' : 372.2e6,
'Canada': 37.59e6,
'Belgium': 11.4e6,
'Denmark': 5.603e6,
'Sweden': 10.12e6,
'Brazil': 209.3e6,
'Australia': 24.6e6,
'Saudi Arabia': 34813.867e3,
}
intervention_strength = {
'No action': 0.,
'Limited action': 0.1,
'Social distancing': 0.35,
'Shelter in place': 0.6,
'Full lockdown': 0.85
}
# Values below are taken from https://population.un.org/wpp/Download/Standard/CSV/.
population = {
'Afghanistan': 38928.341e3,
'Albania': 2877.8e3,
'Algeria': 43851.043e3,
'Andorra': 77.265e3,
'Angola': 32866.268e3,
'Antigua and Barbuda': 97.928e3,
'Argentina': 45195.777e3,
'Armenia': 2963.2340000000004e3,
'Australia': 25499.881e3,
'Austria': 9006.4e3,
'Azerbaijan': 10139.175e3,
'Bahamas': 393.24800000000005e3,
'Bahrain': 1701.5829999999999e3,
'Bangladesh': 164689.383e3,
'Barbados': 287.371e3,
'Belarus': 9449.321e3,
'Belgium': 11589.616000000002e3,
'Belize': 397.621e3,
'Benin': 12123.198e3,
'Bhutan': 771.612e3,
'Bolivia': 11673.028999999999e3,
'Bosnia and Herzegovina': 3280.815e3,
'Brazil': 212559.40899999999e3,
'Bulgaria': 6948.445e3,
'Burkina Faso': 20903.278000000002e3,
'Cabo Verde': 555.988e3,
'Cambodia': 16718.971e3,
'Cameroon': 26545.863999999998e3,
'Canada': 37742.157e3,
'Central African Republic': 4829.764e3,
'Chad': 16425.859e3,
'Chile': 19116.209e3,
'China': 1439323.774e3,
'Colombia': 50882.884000000005e3,
'Costa Rica': 5094.1140000000005e3,
'Croatia': 4105.268e3,
'Cuba': 11326.616000000002e3,
'Cyprus': 1207.361e3,
'Czechia': 10708.982e3,
'Denmark': 5792.203e3,
'Djibouti': 988.002e3,
'Dominica': 71.991e3,
'Dominican Republic': 10847.903999999999e3,
'Ecuador': 17643.06e3,
'Egypt': 102334.403e3,
'El Salvador': 6486.201e3,
'Equatorial Guinea': 1402.985e3,
'Eritrea': 3546.427e3,
'Estonia': 1326.539e3,
'Eswatini': 1160.164e3,
'Ethiopia': 114963.58300000001e3,
'Fiji': 896.444e3,
'Finland': 5540.718000000001e3,
'France': 65273.512e3,
'Gabon': 2225.728e3,
'Gambia': 2416.6639999999998e3,
'Georgia': 3989.175e3,
'Germany': 83783.945e3,
'Ghana': 31072.945e3,
'Greece': 10423.056e3,
'Grenada': 112.51899999999999e3,
'Guatemala': 17915.567e3,
'Guinea': 13132.792e3,
'Guinea-Bissau': 1967.9979999999998e3,
'Guyana': 786.559e3,
'Haiti': 11402.533000000001e3,
'Holy See': 0.809e3,
'Honduras': 9904.608e3,
'Hungary': 9660.35e3,
'Iceland': 341.25e3,
'India': 1380004.385e3,
'Indonesia': 273523.62100000004e3,
'Iran': 83992.95300000001e3,
'Iraq': 40222.503e3,
'Ireland': 4937.795999999999e3,
'Israel': 8655.541e3,
'Italy': 60461.828e3,
'Jamaica': 2961.1609999999996e3,
'Japan': 126476.45800000001e3,
'Jordan': 10203.14e3,
'Kazakhstan': 18776.707e3,
'Kenya': 53771.3e3,
'Kuwait': 4270.563e3,
'Kyrgyzstan': 6524.191e3,
'Laos': 7275.556e3,
'Latvia': 1886.2020000000002e3,
'Lebanon': 6825.441999999999e3,
'Liberia': 5057.677e3,
'Libya': 6871.286999999999e3,
'Liechtenstein': 38.137e3,
'Lithuania': 2722.2909999999997e3,
'Luxembourg': 625.976e3,
'Madagascar': 27691.019e3,
'Malaysia': 32365.998e3,
'Maldives': 540.5419999999999e3,
'Mali': 20250.834e3,
'Malta': 441.539e3,
'Mauritania': 4649.66e3,
'Mauritius': 1271.767e3,
'Mexico': 128932.75300000001e3,
'Monaco': 39.244e3,
'Mongolia': 3278.292e3,
'Montenegro': 628.062e3,
'Morocco': 36910.558e3,
'Mozambique': 31255.435e3,
'Namibia': 2540.916e3,
'Nepal': 29136.807999999997e3,
'Netherlands': 17134.873e3,
'New Zealand': 4822.233e3,
'Nicaragua': 6624.554e3,
'Niger': 24206.636000000002e3,
'Nigeria': 206139.587e3,
'North Macedonia': 2083.38e3,
'Norway': 5421.241999999999e3,
'Oman': 5106.622e3,
'Pakistan': 220892.331e3,
'Panama': 4314.768e3,
'Papua New Guinea': 8947.027e3,
'Paraguay': 7132.53e3,
'Peru': 32971.846e3,
'Philippines': 109581.085e3,
'Poland': 37846.605e3,
'Portugal': 10196.707e3,
'Qatar': 2881.06e3,
'Korea, South': 51269.183e3,
'Romania': 19237.682e3,
'Russia': 145934.46e3,
'Rwanda': 12952.208999999999e3,
'Saint Kitts and Nevis': 53.192e3,
'Saint Lucia': 183.62900000000002e3,
'Saint Vincent and the Grenadines': 110.947e3,
'San Marino': 33.938e3,
'Senegal': 16743.93e3,
'Serbia': 8737.37e3,
'Seychelles': 98.34e3,
'Singapore': 5850.343000000001e3,
'Slovakia': 5459.643e3,
'Slovenia': 2078.9320000000002e3,
'Somalia': 15893.219e3,
'South Africa': 59308.69e3,
'Spain': 46754.782999999996e3,
'Sri Lanka': 21413.25e3,
'Sudan': 43849.269e3,
'Suriname': 586.634e3,
'Sweden': 10099.27e3,
'Switzerland': 8654.618e3,
'Syria': 17500.657e3,
'Thailand': 69799.978e3,
'Timor-Leste': 1318.442e3,
'Togo': 8278.737e3,
'Trinidad and Tobago': 1399.491e3,
'Tunisia': 11818.618e3,
'Turkey': 84339.067e3,
'Uganda': 45741.0e3,
'Ukraine': 43733.759000000005e3,
'United Arab Emirates': 9890.4e3,
'United Kingdom': 67886.004e3,
'US': 331002.647e3,
'Uruguay': 3473.7270000000003e3,
'Uzbekistan': 33469.199e3,
'Venezuela': 28435.943e3,
'Vietnam': 97338.58300000001e3,
'Zambia': 18383.956000000002e3,
'Zimbabwe': 14862.927e3
}
US_state_population = {
'Alabama': 4903185,
'Alaska': 731545,
'Arizona': 7278717,
'Arkansas': 3017804,
'California': 39512223,
'Colorado': 5758736,
'Connecticut': 3565287,
'Delaware': 973764,
'District of Columbia': 705749,
'Florida': 21477737,
'Georgia': 10617423,
'Hawaii': 1415872,
'Idaho': 1787065,
'Illinois': 12671821,
'Indiana': 6732219,
'Iowa': 3155070,
'Kansas': 2913314,
'Kentucky': 4467673,
'Louisiana': 4648794,
'Maine': 1344212,
'Maryland': 6045680,
'Massachusetts': 6892503,
'Michigan': 9986857,
'Minnesota': 5639632,
'Mississippi': 2976149,
'Missouri': 6137428,
'Montana': 1068778,
'Nebraska': 1934408,
'Nevada': 3080156,
'New Hampshire': 1359711,
'New Jersey': 8882190,
'New Mexico': 2096829,
'New York': 19453561,
'North Carolina': 10488084,
'North Dakota': 762062,
'Ohio': 11689100,
'Oklahoma': 3956971,
'Oregon': 4217737,
'Pennsylvania': 12801989,
'Rhode Island': 1059361,
'South Carolina': 5148714,
'South Dakota': 884659,
'Tennessee': 6829174,
'Texas': 28995881,
'Utah': 3205958,
'Vermont': 623989,
'Virginia': 8535519,
'Washington': 7614893,
'West Virginia': 1792147,
'Wisconsin': 5822434,
'Wyoming': 578759,
'Puerto Rico': 3193694
}
us_state_abbrev = {
'Alabama': 'AL',
'Alaska': 'AK',
'American Samoa': 'AS',
'Arizona': 'AZ',
'Arkansas': 'AR',
'California': 'CA',
'Colorado': 'CO',
'Connecticut': 'CT',
'Delaware': 'DE',
'District of Columbia': 'DC',
'Florida': 'FL',
'Georgia': 'GA',
'Guam': 'GU',
'Hawaii': 'HI',
'Idaho': 'ID',
'Illinois': 'IL',
'Indiana': 'IN',
'Iowa': 'IA',
'Kansas': 'KS',
'Kentucky': 'KY',
'Louisiana': 'LA',
'Maine': 'ME',
'Maryland': 'MD',
'Massachusetts': 'MA',
'Michigan': 'MI',
'Minnesota': 'MN',
'Mississippi': 'MS',
'Missouri': 'MO',
'Montana': 'MT',
'Nebraska': 'NE',
'Nevada': 'NV',
'New Hampshire': 'NH',
'New Jersey': 'NJ',
'New Mexico': 'NM',
'New York': 'NY',
'North Carolina': 'NC',
'North Dakota': 'ND',
'Northern Mariana Islands':'MP',
'Ohio': 'OH',
'Oklahoma': 'OK',
'Oregon': 'OR',
'Pennsylvania': 'PA',
'Puerto Rico': 'PR',
'Rhode Island': 'RI',
'South Carolina': 'SC',
'South Dakota': 'SD',
'Tennessee': 'TN',
'Texas': 'TX',
'Utah': 'UT',
'Vermont': 'VT',
'Virgin Islands': 'VI',
'Virginia': 'VA',
'Washington': 'WA',
'West Virginia': 'WV',
'Wisconsin': 'WI',
'Wyoming': 'WY'
}