X-Git-Url: https://git.njae.me.uk/?p=covid19.git;a=blobdiff_plain;f=uk_deaths.md;h=e0077b334078753e5cb299385bf8f8a17e188e1e;hp=76ca621b134af706405f3554c785d3718b2ddcd4;hb=HEAD;hpb=79e379ea62db432275bd0b352122f523a03a9a0e diff --git a/uk_deaths.md b/uk_deaths.md deleted file mode 100644 index 76ca621..0000000 --- a/uk_deaths.md +++ /dev/null @@ -1,372 +0,0 @@ ---- -jupyter: - jupytext: - formats: ipynb,md - text_representation: - extension: .md - format_name: markdown - format_version: '1.2' - jupytext_version: 1.3.4 - kernelspec: - display_name: Python 3 - language: python - name: python3 ---- - -Data from: - -* [Office of National Statistics](https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/weeklyprovisionalfiguresondeathsregisteredinenglandandwales) (Endland and Wales) Weeks start on a Saturday. -* [Northern Ireland Statistics and Research Agency](https://www.nisra.gov.uk/publications/weekly-deaths) (Northern Ireland). Weeks start on a Saturday. Note that the week numbers don't match the England and Wales data. -* [National Records of Scotland](https://www.nrscotland.gov.uk/statistics-and-data/statistics/statistics-by-theme/vital-events/general-publications/weekly-and-monthly-data-on-births-and-deaths/weekly-data-on-births-and-deaths) (Scotland). Note that Scotland uses ISO8601 week numbers, which start on a Monday. - - -```python -import itertools -import collections -import pandas as pd -import numpy as np -from scipy.stats import gmean - -import matplotlib as mpl -import matplotlib.pyplot as plt -%matplotlib inline -``` - -```python -!ls uk-deaths-data -``` - -```python -raw_data_2015 = pd.read_csv('uk-deaths-data/Weekly_Deaths_NI_2015.csv', - parse_dates=[1, 2], dayfirst=True, - index_col=0, - header=[0, 1] - ) -dh15i = raw_data_2015.iloc[:, [2]] -dh15i.columns = ['total_2015'] -# dh15i.head() -``` - -```python -raw_data_2016 = pd.read_csv('uk-deaths-data/Weekly_Deaths_NI_2016.csv', - parse_dates=[1, 2], dayfirst=True, - index_col=0, - header=[0, 1] - ) -dh16i = raw_data_2016.iloc[:, [2]] -dh16i.columns = ['total_2016'] -# dh16i.head() -``` - -```python -raw_data_2017 = pd.read_csv('uk-deaths-data/Weekly_Deaths_NI_2017.csv', - parse_dates=[1, 2], dayfirst=True, - index_col=0, - header=[0, 1] - ) -dh17i = raw_data_2017.iloc[:, [2]] -dh17i.columns = ['total_2017'] -# dh17i.head() -``` - -```python -raw_data_2018 = pd.read_csv('uk-deaths-data/Weekly_Deaths_NI_2018.csv', - parse_dates=[1, 2], dayfirst=True, - index_col=0, - header=[0, 1] - ) -dh18i = raw_data_2018.iloc[:, [2]] -dh18i.columns = ['total_2018'] -# dh18i.head() -``` - -```python -raw_data_2019 = pd.read_csv('uk-deaths-data/Weekly_Deaths_NI_2019.csv', - parse_dates=[1, 2], dayfirst=True, - index_col=0, - header=[0, 1] - ) -dh19i = raw_data_2019.iloc[:, [2]] -dh19i.columns = ['total_2019'] -# dh19i.head() -``` - -```python -raw_data_2020_i = pd.read_csv('uk-deaths-data/Weekly_Deaths_NI_2020.csv', - parse_dates=[1], dayfirst=True, - index_col=0, - header=[0, 1] - ) -deaths_headlines_i = raw_data_2020_i.iloc[:, [1]] -deaths_headlines_i.columns = ['total_2020'] -deaths_headlines_i.head() -``` - -```python - -``` - -```python - -``` - -```python -raw_data_s = pd.read_csv('uk-deaths-data/weekly-deaths-april-20-scotland.csv', - index_col=0, - header=0, - skiprows=2 - ) -# raw_data_s -``` - -```python -deaths_headlines_s = raw_data_s[reversed('2015 2016 2017 2018 2019 2020'.split())] -deaths_headlines_s.columns = ['total_' + c for c in deaths_headlines_s.columns] -deaths_headlines_s.reset_index(drop=True, inplace=True) -deaths_headlines_s.index = deaths_headlines_s.index + 1 -deaths_headlines_s -``` - -```python - -``` - -```python - -``` - -```python - -``` - -```python - -``` - -```python - -``` - -```python -raw_data_2020 = pd.read_csv('uk-deaths-data/publishedweek182020.csv', - parse_dates=[1], dayfirst=True, - index_col=0, - header=[0, 1]) -``` - -```python -# raw_data_2020.head() -``` - -```python -raw_data_2020['W92000004', 'Wales'] -``` - -```python -raw_data_2019 = pd.read_csv('uk-deaths-data/publishedweek522019.csv', - parse_dates=[1], dayfirst=True, - index_col=0, - header=[0, 1]) -# raw_data_2019.head() -``` - -```python -raw_data_2018 = pd.read_csv('uk-deaths-data/publishedweek522018.csv', - parse_dates=[1], dayfirst=True, - index_col=0, - header=[0, 1]) -# raw_data_2018.head() -``` - -```python -raw_data_2017 = pd.read_csv('uk-deaths-data/publishedweek522017.csv', - parse_dates=[1], dayfirst=True, - index_col=0, - header=[0, 1]) -# raw_data_2017.head() -``` - -```python -raw_data_2016 = pd.read_csv('uk-deaths-data/publishedweek522016.csv', - parse_dates=[1], dayfirst=True, - index_col=0, - header=[0, 1]) -# raw_data_2016.head() -``` - -```python -raw_data_2015 = pd.read_csv('uk-deaths-data/publishedweek2015.csv', - parse_dates=[1], dayfirst=True, - index_col=0, - header=[0, 1]) -# raw_data_2015.head() -``` - -```python -deaths_headlines_e = raw_data_2020.iloc[:, [1]] -deaths_headlines_e.columns = ['total_2020'] -deaths_headlines_w = raw_data_2020['W92000004'] -deaths_headlines_e.columns = ['total_2020'] -deaths_headlines_w.columns = ['total_2020'] -deaths_headlines_e.total_2020 -= deaths_headlines_w.total_2020 -deaths_headlines_e.head() -deaths_headlines_e -``` - -```python -dh19e = raw_data_2019.iloc[:, [1]] -dh19w = raw_data_2019['W92000004'] -dh19e.columns = ['total_2019'] -dh19w.columns = ['total_2019'] -dh19e.total_2019 -= dh19w.total_2019 -dh19e.head() -``` - -```python -dh19w.head() -``` - -```python -dh18e = raw_data_2018.iloc[:, [1]] -dh18w = raw_data_2018['W92000004'] -dh18e.columns = ['total_2018'] -dh18w.columns = ['total_2018'] -dh18e.total_2018 -= dh18w.total_2018 -# dh18e.head() -``` - -```python -dh17e = raw_data_2017.iloc[:, [1]] -dh17w = raw_data_2017['W92000004'] -dh17e.columns = ['total_2017'] -dh17w.columns = ['total_2017'] -dh17e.total_2017 -= dh17w.total_2017 -# dh17e.head() -``` - -```python -dh16e = raw_data_2016.iloc[:, [1]] -dh16w = raw_data_2016['W92000004'] -dh16e.columns = ['total_2016'] -dh16w.columns = ['total_2016'] -dh16e.total_2016 -= dh16w.total_2016 -# dh16e.head() -``` - -```python -dh15e = raw_data_2015.iloc[:, [1]] -dh15w = raw_data_2015['W92000004'] -dh15e.columns = ['total_2015'] -dh15w.columns = ['total_2015'] -dh15e.total_2015 -= dh15w.total_2015 -# dh15e.head() -``` - -```python -# dh18 = raw_data_2018.iloc[:, [1, 2]] -# dh18.columns = ['total_2018', 'total_previous'] -# # dh18.head() -``` - -```python -deaths_headlines_e = deaths_headlines_e.merge(dh19e['total_2019'], how='outer', left_index=True, right_index=True) -deaths_headlines_e = deaths_headlines_e.merge(dh18e['total_2018'], how='outer', left_index=True, right_index=True) -deaths_headlines_e = deaths_headlines_e.merge(dh17e['total_2017'], how='outer', left_index=True, right_index=True) -deaths_headlines_e = deaths_headlines_e.merge(dh16e['total_2016'], how='outer', left_index=True, right_index=True) -# deaths_headlines = deaths_headlines.merge(dh15['total_2015'], how='outer', left_index=True, right_index=True) -deaths_headlines_e = deaths_headlines_e.merge(dh15e['total_2015'], how='left', left_index=True, right_index=True) -deaths_headlines_e -``` - -```python -deaths_headlines_s = raw_data_s[reversed('2015 2016 2017 2018 2019 2020'.split())] -deaths_headlines_s.columns = ['total_' + c for c in deaths_headlines_s.columns] -deaths_headlines_s.reset_index(drop=True, inplace=True) -deaths_headlines_s.index = deaths_headlines_s.index + 1 -deaths_headlines_s = deaths_headlines_s.loc[1:52] -deaths_headlines_s -``` - -```python -deaths_headlines_w = deaths_headlines_w.merge(dh19w['total_2019'], how='outer', left_index=True, right_index=True) -deaths_headlines_w = deaths_headlines_w.merge(dh18w['total_2018'], how='outer', left_index=True, right_index=True) -deaths_headlines_w = deaths_headlines_w.merge(dh17w['total_2017'], how='outer', left_index=True, right_index=True) -deaths_headlines_w = deaths_headlines_w.merge(dh16w['total_2016'], how='outer', left_index=True, right_index=True) -# deaths_headlines = deaths_headlines.merge(dh15['total_2015'], how='outer', left_index=True, right_index=True) -deaths_headlines_w = deaths_headlines_w.merge(dh15w['total_2015'], how='left', left_index=True, right_index=True) -deaths_headlines_w -``` - -```python -deaths_headlines_i = deaths_headlines_i.merge(dh19i['total_2019'], how='outer', left_index=True, right_index=True) -deaths_headlines_i = deaths_headlines_i.merge(dh18i['total_2018'], how='outer', left_index=True, right_index=True) -deaths_headlines_i = deaths_headlines_i.merge(dh17i['total_2017'], how='outer', left_index=True, right_index=True) -deaths_headlines_i = deaths_headlines_i.merge(dh16i['total_2016'], how='outer', left_index=True, right_index=True) -deaths_headlines_i = deaths_headlines_i.merge(dh15i['total_2015'], how='left', left_index=True, right_index=True) -deaths_headlines_i -``` - -```python -deaths_headlines = deaths_headlines_e + deaths_headlines_w + deaths_headlines_i + deaths_headlines_s -deaths_headlines -``` - -```python -deaths_headlines['previous_mean'] = deaths_headlines['total_2019 total_2018 total_2017 total_2016 total_2015'.split()].apply(np.mean, axis=1) -deaths_headlines -``` - -```python -deaths_headlines['total_2020 total_2019 total_2018 total_2017 total_2016 total_2015'.split()].plot(figsize=(10, 8)) -``` - -```python -Radar plot code taken f -fig = plt.figure(figsize=(10, 10)) -ax = fig.add_subplot(111, projection="polar") - -theta = np.roll( - np.flip( - np.arange(len(deaths_headlines))/float(len(deaths_headlines))*2.*np.pi), - 14) -# l15, = ax.plot(theta, deaths_headlines['total_2015'], color="#b56363", label="2015") # 0 -# l16, = ax.plot(theta, deaths_headlines['total_2016'], color="#a4b563", label="2016") # 72 -# l17, = ax.plot(theta, deaths_headlines['total_2017'], color="#63b584", label="2017") # 144 -# l18, = ax.plot(theta, deaths_headlines['total_2018'], color="#6384b5", label="2018") # 216 -# l19, = ax.plot(theta, deaths_headlines['total_2019'], color="#a4635b", label="2019") # 288 -l15, = ax.plot(theta, deaths_headlines['total_2015'], color="#e47d7d", label="2015") # 0 -l16, = ax.plot(theta, deaths_headlines['total_2016'], color="#afc169", label="2016") # 72 , d0e47d -l17, = ax.plot(theta, deaths_headlines['total_2017'], color="#7de4a6", label="2017") # 144 -l18, = ax.plot(theta, deaths_headlines['total_2018'], color="#7da6e4", label="2018") # 216 -l19, = ax.plot(theta, deaths_headlines['total_2019'], color="#d07de4", label="2019") # 288 - -lmean, = ax.plot(theta, deaths_headlines['previous_mean'], color="black", linestyle='dashed', label="mean") - -l20, = ax.plot(theta, deaths_headlines['total_2020'], color="red", label="2020") - -# deaths_headlines.total_2019.plot(ax=ax) - -def _closeline(line): - x, y = line.get_data() - x = np.concatenate((x, [x[0]])) - y = np.concatenate((y, [y[0]])) - line.set_data(x, y) - -[_closeline(l) for l in [l19, l18, l17, l16, l15, lmean]] - - -ax.set_xticks(theta) -ax.set_xticklabels(deaths_headlines.index) -plt.legend() -plt.title("Deaths by week over years, all UK") -plt.savefig('deaths-radar.png') -plt.show() -``` - -```python -(deaths_headlines.loc[12:].total_2020 - deaths_headlines.loc[12:].previous_mean).sum() -``` - -```python - -```