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