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WorkVaccines.py
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# -*- coding: utf-8 -*-
"""
Created on Mon Apr 26 08:07:05 2021
@author: 212367548
"""
import pandas as pd
import datetime
from plotly.offline import plot as pplot
import plotly.express as px
import os
import datetime
import covid
from tableauscraper import TableauScraper as TS
#%% Vaccination data
# from Our World In Data github, recording CDC data
vax_github = 'https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/vaccinations/us_state_vaccinations.csv'
vax_local = 'C:\\dev\\covid-wisconsin\\data\\vaccinations\\vax-cdc.csv'
vax_df = pd.read_csv(vax_github, converters={'date': pd.to_datetime})
# vax_offline = 'data/vaccinations/us_state_vaccinations.csv'
# vax_df = pd.read_csv(vax_offline, converters={'date': pd.to_datetime})
vax_wi = vax_df[vax_df.location == 'Wisconsin']
vax_us = vax_df[vax_df.location == 'United States']
daily = vax_wi.set_index('date').drop('location', axis=1).diff()
avg7 = daily.rolling(7).mean()
vax_diff = vax_us.set_index('date')['people_vaccinated'].diff()
vax_diff.plot(y='people_vaccinated')
#%% Plots
vax_wi.plot(x='date', y=['total_distributed', 'total_vaccinations'])
vax_wi.plot(x='date', y='share_doses_used')
vax_wi.plot(x='date', y=['people_fully_vaccinated_per_hundred', 'people_vaccinated_per_hundred'])
daily.plot(y=['total_distributed', 'total_vaccinations'])
#%% Plot vax by age group from WI DHS data
vax_age_file = 'data\\vaccinations\\Vax-Age-WI.csv'
vax_age = pd.read_csv(vax_age_file, converters={'Reporting date': pd.to_datetime})
vax_age.pivot(index='Reporting date', columns='Age group', values='Initiated %').plot()
#%% Same for race
vax_race_file = 'data\\vaccinations\\Vax-Race-WI.csv'
vax_race = pd.read_csv(vax_race_file, converters={'Reporting date': pd.to_datetime})
vax_race.pivot(index='Reporting date', columns='Race', values='Initiated %').plot()
#%% administered by day from DHS
url = 'https://bi.wisconsin.gov/t/DHS/views/COVID-19VaccineAdministration/Allocated?:embed_code_version=3&:embed=y&:loadOrderID=0&:display_spinner=no&:showAppBanner=false&:display_count=n&:showVizHome=n&:origin=viz_share_link'
ts = TS()
# ts = loads_with_retries(ts, url, 3)
ts.loads(url)
allocation_dash = ts.getWorkbook()
dhs = allocation_dash.getWorksheet('AdministeredByDay').data
col_rename={'SUM(Immunization Count)-value': 'doses',
# 'SUM(Immunization Count)-alias': 'doses 7-day',
'DAY(Vaccination Date)-value': 'Date'}
dhs = dhs[col_rename.keys()]
dhs = dhs.rename(columns=col_rename)
dhs.Date = pd.to_datetime(dhs.Date)
dhs['total doses'] = dhs.doses.cumsum()
dhs = dhs.set_index('Date')
#%% compare cdc and dhs
vax_wi.loc[:, 'date -2'] = vax_wi['date'].copy() - datetime.timedelta(days=2)
dhs['CDC, reported date -2 days'] = vax_wi.set_index('date -2')['total_vaccinations']
dhs['WI DHS, administered date'] = dhs['total doses']
dhs.diff().plot(y=['CDC, reported date -2 days', 'WI DHS, administered date'], title='Doses per day')
dhs.plot(y=['CDC, reported date -2 days', 'WI DHS, administered date'], title='Total vaccine doses in WI')