uk_cases_and_deaths.py

   1 #!/usr/bin/env python
   2 # coding: utf-8
   3 # %%
   4 import itertools
   5 import collections
   6 import json
   7 import pandas as pd
   8 import numpy as np
   9 from scipy.stats import gmean
  10 import datetime
  11
  12 import sqlalchemy
  13
  14 import matplotlib as mpl
  15 import matplotlib.pyplot as plt
  16 plt.ioff()
  17 # # %matplotlib inline
  18
  19
  20 # %%
  21 connection_string = 'postgresql://covid:3NbjJTkT63@localhost/covid'
  22
  23
  24 # %%
  25 engine = sqlalchemy.create_engine(connection_string)
  26
  27
  28 # %%
  29 qstr = '''select uk_data.date
  30     , uk_data.new_cases, uk_data_7.new_cases as new_cases_7
  31     , uk_data.new_deaths, uk_data_7.new_deaths as new_deaths_7
  32     from uk_data left outer join uk_data_7 using (date)
  33     order by uk_data.date'''
  34 uk_data = pd.read_sql_query(qstr, engine,
  35     index_col='date',
  36     parse_dates = ['date'])
  37
  38 # %%
  39 ax = uk_data.loc['2020-03-10':, ['new_cases', 'new_cases_7']].plot(
  40     style={'new_cases': "#e4e4e4",
  41            'new_cases_7': 'k'},
  42     figsize=(10, 8),
  43     legend=False,
  44     title="New cases and new deaths")
  45
  46 # ax.set_title('Fraction of tests with positive results')
  47 ax.legend(['New cases', 'New cases, 7 day moving average'], loc='upper left')
  48 ax.set_ylabel('New cases')
  49
  50 ax2 = ax.twinx()
  51 ax2 = uk_data.loc['2020-03-10':, ['new_deaths','new_deaths_7']].plot(
  52     ax=ax2,
  53     secondary_y=['new_deaths', 'new_deaths_7'],
  54     style={'new_deaths': "#ffe4e4",
  55            'new_deaths_7': 'r'},
  56     legend=False)
  57 ax2.legend(['New deaths', 'New deaths, 7 day moving average'], loc='best')
  58 ax2.set_ylabel('New cases')
  59 plt.savefig('cases_and_deaths.png')
  60
  61
  62 # %%
  63 ax = uk_data.iloc[-60:][['new_cases', 'new_cases_7']].plot(
  64     style={'new_cases': "#e4e4e4",
  65            'new_cases_7': 'k'},
  66     figsize=(10, 8),
  67     legend=False,
  68     title="New cases and new deaths")
  69
  70 # ax.set_title('Fraction of tests with positive results')
  71 ax.legend(['New cases', 'New cases, 7 day moving average'], loc='upper left')
  72 ax.set_ylabel('New cases')
  73
  74
  75 ax2 = ax.twinx()
  76 ax2 = uk_data.iloc[-60:][['new_deaths','new_deaths_7']].plot(
  77     ax=ax2,
  78     secondary_y=['new_deaths', 'new_deaths_7'],
  79     style={'new_deaths': "#ffe4e4",
  80            'new_deaths_7': 'r'},
  81     legend=False)
  82 ax2.legend(['New deaths', 'New deaths, 7 day moving average'], loc='best')
  83 ax2.set_ylabel('New cases')
  84 plt.savefig('cases_and_deaths_last_60_days.png')
  85
  86
  87 # %%
  88
  89
  90
  91