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UpdateOutcomePlots.py
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# -*- coding: utf-8 -*-
"""
Work on new plots for monitoring the situation.
Created on Wed Jun 30 10:48:03 2021
@author: 212367548
"""
import datetime
import os
import covid
from tableauscraper import TableauScraper as TS
ts = TS()
#%% Deaths / cases plot
case_df = covid.scrape_widash_cases()
death_df = covid.scrape_widash_deaths()
hosp_df = covid.download_hhs_data_wi()
#%% Put all data into one DF
plotdata = case_df[['Date', 'Confirmed']]
plotdata = plotdata.rename(columns={'Confirmed': 'Cases'})
plotdata = plotdata.set_index('Date')
plotdata['Deaths'] = death_df.set_index('Date')['Confirmed']
plotdata['Admissions'] = hosp_df.set_index('Date')['previous_day_admission_adult_covid_confirmed']
plotdata = plotdata.reset_index()
#%% Function to add shading to preliminary area of plot
def shade_preliminary(fig, x0, x1):
# shading applied to the x range between x0 and x1
fig.add_shape(
type="rect",
xref='x', x0=x0, x1=x1,
yref='paper', y0=0, y1=1,
line_color='rgba(0,0,0,0)',
fillcolor='rgba(0,0,0,0.2)',
)
fig.add_annotation(
xanchor='right', xref='x', x=x0,
yanchor='top', yref='paper', y=1,
text='Preliminary<br>data',
font_color='rgb(0.5,0.5,0.5)',
align='right',
showarrow=False,
)
#%% Plot Deaths / Cases
# parameters for comparison
lag = 12
cfr = 0.012
# Make a plot
plotpath = '.\\docs\\_includes\\plotly'
savefile = plotpath+'\\Deaths-Cases-WI.html'
fig = covid.plotly_twolines(
plotdata,
'Deaths',
'Cases',
plotcolors=['firebrick', 'steelblue', 'rosybrown'],
secondary_scale=1/cfr,
# date_min=datetime.datetime(2021,1,15),
range_max=160,
col1_mode='avg-bar',
col2_mode='avg',
plotlabels = {'title': 'Deaths vs Cases - WI<br>(CFR '+str(cfr*100)+'%)',
'yaxis': 'Deaths',
'yaxis_secondary': 'Cases',
},
savefile=savefile,
showfig=False,
)
fig.update_xaxes(title_text='Date of death / Date of test')
# shade the recent data using custom function
shade_days = 14
end_date = plotdata.Date.max()
start_date = end_date - datetime.timedelta(days=shade_days)
shade_preliminary(fig, start_date, end_date)
fig.write_html(
file=savefile,
default_height=480,
include_plotlyjs='cdn',
)
os.startfile(savefile)
#%% Hospitalization plot
# Make a plot
plotpath = '.\\docs\\_includes\\plotly'
savefile = plotpath+'\\Hosp-Cases-WI.html'
hrate = 0.09
fig = covid.plotly_twolines(
plotdata,
'Admissions',
'Cases',
plotcolors=['darkorange', 'steelblue', 'burlywood'],
secondary_scale=1/hrate,
# date_min=datetime.datetime(2021,1,15),
range_max=1200,
col1_mode='avg-bar',
col2_mode='avg',
plotlabels = {'title': 'Hospital Admissions vs Cases - WI',
'yaxis': 'Admissions',
'yaxis_secondary': 'Cases',
},
savefile=savefile,
showfig=False,
)
fig.update_xaxes(title_text='Date of admission / Date of test')
# shade the recent data using custom function
shade_days = 14
end_date = plotdata.Date.max()
start_date = end_date - datetime.timedelta(days=shade_days)
shade_preliminary(fig, start_date, end_date)
fig.write_html(
file=savefile,
default_height=480,
include_plotlyjs='cdn',
)
os.startfile(savefile)