--- /dev/null
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "source": [
+ "Data from [European Centre for Disease Prevention and Control](https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 192,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "The sql extension is already loaded. To reload it, use:\n",
+ " %reload_ext sql\n"
+ ]
+ }
+ ],
+ "source": [
+ "import itertools\n",
+ "import collections\n",
+ "import json\n",
+ "import pandas as pd\n",
+ "import numpy as np\n",
+ "from scipy.stats import gmean\n",
+ "import datetime\n",
+ "\n",
+ "import matplotlib as mpl\n",
+ "import matplotlib.pyplot as plt\n",
+ "%matplotlib inline\n",
+ "%load_ext sql"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 193,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "connection_string = 'postgresql://covid:3NbjJTkT63@localhost/covid'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 194,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "'Connected: covid@covid'"
+ ]
+ },
+ "execution_count": 194,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "%sql $connection_string"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 195,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "# DEATH_COUNT_THRESHOLD = 10\n",
+ "COUNTRIES_CORE = tuple('IT DE UK ES IE FR BE'.split())\n",
+ "# COUNTRIES_NORDIC = 'SE NO DK FI UK'.split()\n",
+ "# COUNTRIES_FRIENDS = 'IT UK ES BE SI MX'.split()\n",
+ "# # COUNTRIES_FRIENDS = 'IT UK ES BE SI PT'.split()\n",
+ "\n",
+ "# COUNTRIES_AMERICAS = ['AG', 'AR', 'AW', 'BS', 'BB', 'BZ', 'BM', 'BO', 'BR', 'VG', 'KY', # excluding Canada and USA\n",
+ "# 'CL', 'CO', 'CR', 'CU', 'CW', 'DM', 'DO', 'EC', 'SV', 'GL', 'GD', 'GT',\n",
+ "# 'GY', 'HT', 'HN', 'JM', 'MX', 'MS', 'NI', 'PA', 'PY', 'PE', 'PR', 'KN',\n",
+ "# 'LC', 'VC', 'SX', 'SR', 'TT', 'TC', 'VI', 'UY', 'VE']\n",
+ "# COUNTRIES_OF_INTEREST = list(set(COUNTRIES_CORE + COUNTRIES_FRIENDS))\n",
+ "# COUNTRIES_ALL = list(set(COUNTRIES_CORE + COUNTRIES_FRIENDS + COUNTRIES_NORDIC + COUNTRIES_AMERICAS))"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "source": [
+ "# Write results to summary file"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 196,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " * postgresql://covid:***@localhost/covid\n",
+ "1 rows affected.\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "datetime.date(2021, 1, 26)"
+ ]
+ },
+ "execution_count": 196,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "last_uk_date = %sql select date from uk_data order by date desc limit 1\n",
+ "last_uk_date = last_uk_date[0][0]\n",
+ "last_uk_date"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 197,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " * postgresql://covid:***@localhost/covid\n",
+ "1 rows affected.\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "datetime.date(2021, 1, 18)"
+ ]
+ },
+ "execution_count": 197,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "last_intl_date = %sql select report_date from weekly_cases order by report_date desc limit 1\n",
+ "last_intl_date = last_intl_date[0][0]\n",
+ "last_intl_date"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 198,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " * postgresql://covid:***@localhost/covid\n",
+ "390 rows affected.\n",
+ "Returning data to local variable results\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%sql results << select date, new_cases, new_deaths \n",
+ "from uk_data \n",
+ "order by date"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 199,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "<div>\n",
+ "<style scoped>\n",
+ " .dataframe tbody tr th:only-of-type {\n",
+ " vertical-align: middle;\n",
+ " }\n",
+ "\n",
+ " .dataframe tbody tr th {\n",
+ " vertical-align: top;\n",
+ " }\n",
+ "\n",
+ " .dataframe thead th {\n",
+ " text-align: right;\n",
+ " }\n",
+ "</style>\n",
+ "<table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th></th>\n",
+ " <th>new_cases</th>\n",
+ " <th>new_deaths</th>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>date</th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>2021-01-17</th>\n",
+ " <td>28875.0</td>\n",
+ " <td>671</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-18</th>\n",
+ " <td>44732.0</td>\n",
+ " <td>599</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-19</th>\n",
+ " <td>39311.0</td>\n",
+ " <td>1610</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-20</th>\n",
+ " <td>35015.0</td>\n",
+ " <td>1820</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-21</th>\n",
+ " <td>31430.0</td>\n",
+ " <td>1290</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-22</th>\n",
+ " <td>29094.0</td>\n",
+ " <td>1401</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-23</th>\n",
+ " <td>20495.0</td>\n",
+ " <td>1348</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-24</th>\n",
+ " <td>14266.0</td>\n",
+ " <td>610</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-25</th>\n",
+ " <td>4482.0</td>\n",
+ " <td>592</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2021-01-26</th>\n",
+ " <td>NaN</td>\n",
+ " <td>1631</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " new_cases new_deaths\n",
+ "date \n",
+ "2021-01-17 28875.0 671\n",
+ "2021-01-18 44732.0 599\n",
+ "2021-01-19 39311.0 1610\n",
+ "2021-01-20 35015.0 1820\n",
+ "2021-01-21 31430.0 1290\n",
+ "2021-01-22 29094.0 1401\n",
+ "2021-01-23 20495.0 1348\n",
+ "2021-01-24 14266.0 610\n",
+ "2021-01-25 4482.0 592\n",
+ "2021-01-26 NaN 1631"
+ ]
+ },
+ "execution_count": 199,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "uk_data = results.DataFrame()\n",
+ "uk_data['date'] = uk_data.date.astype('datetime64[ns]')\n",
+ "uk_data.set_index('date', inplace=True)\n",
+ "uk_data.tail(10)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 200,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " * postgresql://covid:***@localhost/covid\n",
+ "1 rows affected.\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "datetime.date(2021, 1, 26)"
+ ]
+ },
+ "execution_count": 200,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "most_recent_uk_date = %sql select max(date) from uk_data\n",
+ "most_recent_uk_date = most_recent_uk_date[0][0]\n",
+ "most_recent_uk_date"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 201,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " * postgresql://covid:***@localhost/covid\n",
+ "7 rows affected.\n",
+ "Returning data to local variable results\n"
+ ]
+ }
+ ],
+ "source": [
+ "%%sql results << select geo_id, country_name, culm_deaths \n",
+ "from weekly_cases join countries using (geo_id)\n",
+ "where geo_id in :COUNTRIES_CORE \n",
+ " and (geo_id, report_date) in (select geo_id, max(report_date) from weekly_cases group by geo_id)\n",
+ "order by geo_id"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 202,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "datetime.date(2020, 12, 27)"
+ ]
+ },
+ "execution_count": 202,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "thirty_days_ago = most_recent_uk_date - datetime.timedelta(days=30)\n",
+ "thirty_days_ago"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 203,
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ " * postgresql://covid:***@localhost/covid\n",
+ "1 rows affected.\n",
+ " * postgresql://covid:***@localhost/covid\n",
+ "1 rows affected.\n",
+ " * postgresql://covid:***@localhost/covid\n",
+ "1 rows affected.\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "(100184, 29366, 1283174)"
+ ]
+ },
+ "execution_count": 203,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# thirty_days_ago = most_recent_uk_date - datetime.interval(days=30)\n",
+ "total_uk_deaths = %sql select sum(new_deaths) from uk_data\n",
+ "total_uk_deaths = total_uk_deaths[0][0]\n",
+ "deaths_in_past_month = %sql select sum(new_deaths) from uk_data where date > :thirty_days_ago\n",
+ "deaths_in_past_month = deaths_in_past_month[0][0]\n",
+ "cases_in_past_month = %sql select sum(new_cases) from uk_data where date > :thirty_days_ago\n",
+ "cases_in_past_month = cases_in_past_month[0][0]\n",
+ "total_uk_deaths, deaths_in_past_month, cases_in_past_month"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 204,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'w') as f:\n",
+ " f.write('% Covid death data summary\\n')\n",
+ " f.write('% Neil Smith\\n')\n",
+ " f.write(f'% Created on {datetime.datetime.now().strftime(\"%Y-%m-%d\")}\\n')\n",
+ " f.write('\\n') \n",
+ " f.write(f'> Last UK data from {last_uk_date.strftime(\"%d %b %Y\")}. ')\n",
+ " f.write(f' Last international data from {last_intl_date.strftime(\"%d %b %Y\")}.\\n')\n",
+ " f.write('\\n') "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 205,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'a') as f:\n",
+ " f.write('## Headlines (UK data)\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('| []() | |\\n')\n",
+ " f.write('|:---|---:|\\n')\n",
+ " f.write(f'| Deaths reported so far | {total_uk_deaths} | \\n')\n",
+ " f.write(f'| Deaths in last 30 days | {deaths_in_past_month} | \\n')\n",
+ " f.write(f'| Cases in last 30 days | {cases_in_past_month} | \\n')\n",
+ "# f.write(f'| Total Covid deaths to date (estimated) | {uk_deaths_to_date:.0f} |\\n')\n",
+ " f.write('\\n')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 206,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'a') as f:\n",
+ " f.write('## International comparison\\n')\n",
+ " f.write('\\n')\n",
+ " f.write(f'Based on weekly data. Last data from {last_intl_date.strftime(\"%d %b %Y\")}\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('### Total deaths\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('| Country ID | Country name | Total deaths |\\n')\n",
+ " f.write('|:-----------|:-------------|-------------:|\\n')\n",
+ " for c_id, c_name, t_deaths in results:\n",
+ " f.write(f'| {c_id} | {c_name} | {t_deaths} |\\n')\n",
+ " f.write('\\n')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 207,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "# with open('covid_summary.md', 'a') as f:\n",
+ "# f.write('## All-causes deaths, UK\\n')\n",
+ "# f.write('\\n')\n",
+ "# f.write('\\n')\n",
+ "# f.write('\\n')\n",
+ "# f.write('### True deaths\\n')\n",
+ "# f.write('\\n')\n",
+ "# f.write(f'The number of deaths reported in official statistics, {uk_covid_deaths}, is an underestimate '\n",
+ "# 'of the true number of Covid deaths.\\n'\n",
+ "# 'This is especially true early in the pandemic, approximately March to May 2020.\\n')\n",
+ "# f.write('We can get a better understanding of the impact of Covid by looking at the number of deaths, '\n",
+ "# 'over and above what would be expected at each week of the year.\\n')\n",
+ "# f.write(f'The ONS (and other bodies in Scotland and Northern Ireland) have released data on the number of deaths '\n",
+ "# f'up to {pd.to_datetime(excess_deaths_data[\"end_date\"]).strftime(\"%d %B %Y\")}.\\n\\n')\n",
+ "# f.write('If, for each of those weeks, I take the largest of the excess deaths or the reported Covid deaths, ')\n",
+ "# f.write(f'I estimate there have been **{uk_deaths_to_date}** total deaths so far.\\n')\n",
+ "# f.write('\\n')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 208,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'a') as f:\n",
+ " f.write('### Deaths per week\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 209,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'a') as f:\n",
+ " f.write('## UK data\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('### Total deaths\\n')\n",
+ " f.write('\\n')\n",
+ " f.write(f'Deaths reported up to {last_uk_date.strftime(\"%d %b %Y\")}: {total_uk_deaths}\\n')\n",
+ " f.write('\\n') \n",
+ " f.write('\\n')\n",
+ " f.write('\\n') \n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 210,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('hospital_normalisation_date.json') as f:\n",
+ " hospital_normalisation_date_data = json.load(f)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 211,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'a') as f:\n",
+ " f.write('### Hospital care\\n')\n",
+ " f.write(f'Based on a 7-day moving average\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('Due to the large scale differences between the three '\n",
+ " 'measures, they are all normalised to show changes ')\n",
+ " f.write(f'since {pd.to_datetime(hospital_normalisation_date_data[\"hospital_normalisation_date\"]).strftime(\"%d %B %Y\")}.\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('People in hospital, and on mechanical ventilators\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 212,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'a') as f:\n",
+ " f.write('### Testing effectiveness\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('A question about testing is whether more detected cases is a result of more tests being '\n",
+ " 'done or is because the number of cases is increasing. One way of telling the differeence '\n",
+ " 'is by looking at the fraction of tests that are positive.\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('Numbers of positive tests and cases, '\n",
+ " '7-day moving average.\\n'\n",
+ " 'Note the different y-axes\\n')\n",
+ " f.write('\\n') \n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('Fraction of tests with a positive result, both daily figures and '\n",
+ " '7-day moving average.\\n')\n",
+ " f.write('\\n') \n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('The trajectory of tests done vs fraction positive tests.\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('Points higher indicate more tests; points to the right indicate more positive tests.'\n",
+ " 'More tests being done with the same infection prevelance will move the point up '\n",
+ " 'and to the left.\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('\\n')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 213,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('covid_summary.md', 'a') as f:\n",
+ " f.write('# Data sources\\n')\n",
+ " f.write('\\n')\n",
+ " f.write('> Covid data from [European Centre for Disease Prevention and Control](https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide)\\n')\n",
+ " f.write('\\n') \n",
+ " f.write(\"\"\"> Population data from:\n",
+ "\n",
+ "* [Office of National Statistics](https://www.ons.gov.uk/peoplepopulationandcommunity/birthsdeathsandmarriages/deaths/datasets/weeklyprovisionalfiguresondeathsregisteredinenglandandwales) (Endland and Wales) Weeks start on a Saturday.\n",
+ "* [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.\n",
+ "* [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.\"\"\")\n",
+ " \n",
+ " f.write('\\n\\n')\n",
+ " f.write('> [Source code available](https://git.njae.me.uk/?p=covid19.git;a=tree)\\n')\n",
+ " f.write('\\n') \n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 214,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "!pandoc --toc -s covid_summary.md > covid_summary.html"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 215,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "covid_summary.html 100% 10KB 287.3KB/s 00:00 \n",
+ "covid_deaths_total_linear.png 100% 45KB 1.8MB/s 00:00 \n",
+ "cases_and_deaths.png 100% 62KB 5.3MB/s 00:00 \n",
+ "cases_and_deaths_last_60_days.png 100% 62KB 8.4MB/s 00:00 \n",
+ "deaths-radar-2020.png 100% 199KB 5.4MB/s 00:00 \n",
+ "covid_deaths_per_week.png 100% 61KB 8.0MB/s 00:00 \n",
+ "fraction_positive_tests.png 100% 59KB 2.8MB/s 00:00 \n",
+ "tests_and_cases.png 100% 40KB 5.4MB/s 00:00 \n",
+ "deaths_by_date_last_6_weeks.png 100% 33KB 5.4MB/s 00:00 \n",
+ "fraction_positive_tests_vs_tests.png 100% 41KB 7.7MB/s 00:00 \n",
+ "tests_vs_fraction_positive_animation.png 100% 1982KB 10.3MB/s 00:00 \n",
+ "people_in_hospital.png 100% 42KB 8.0MB/s 00:00 \n",
+ "cases_admissions_deaths.png 100% 44KB 2.3MB/s 00:00 \n"
+ ]
+ }
+ ],
+ "source": [
+ "!scp covid_summary.html neil@ogedei:/var/www/scripts.njae.me.uk/covid/index.html\n",
+ "!scp covid_deaths_total_linear.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp cases_and_deaths.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp cases_and_deaths_last_60_days.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "# !scp deaths-radar.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp deaths-radar-2020.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp covid_deaths_per_week.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp fraction_positive_tests.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/ \n",
+ "!scp tests_and_cases.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp deaths_by_date_last_6_weeks.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp fraction_positive_tests_vs_tests.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp tests_vs_fraction_positive_animation.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/ \n",
+ "!scp people_in_hospital.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp cases_admissions_deaths.png neil@ogedei:/var/www/scripts.njae.me.uk/covid/"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 216,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "with open('uk_covid_deaths.js', 'w') as f:\n",
+ " f.write(f\"document.write('{total_uk_deaths}');\")\n",
+ " \n",
+ "with open('uk_deaths_30_days.js', 'w') as f:\n",
+ " f.write(f\"document.write('{deaths_in_past_month}');\")\n",
+ "\n",
+ "with open('uk_cases_30_days.js', 'w') as f:\n",
+ " f.write(f\"document.write('{cases_in_past_month}');\") \n",
+ " \n",
+ "# with open('estimated_total_deaths.js', 'w') as f:\n",
+ "# f.write(f\"document.write('{uk_deaths_to_date:.0f}');\")\n",
+ "\n",
+ "# edut = pd.to_datetime(excess_deaths_data[\"end_date\"]).strftime('%d %B %Y')\n",
+ "# with open('excess_deaths_upto.js', 'w') as f:\n",
+ "# f.write(f\"document.write('{edut}');\")\n",
+ " \n",
+ "with open('last_uk_date.js', 'w') as f:\n",
+ " f.write(f\"document.write('{pd.to_datetime(last_uk_date).strftime('%d %B %Y')}');\")\n",
+ "\n",
+ "with open('last_intl_date.js', 'w') as f:\n",
+ " f.write(f\"document.write('{pd.to_datetime(last_intl_date).strftime('%d %B %Y')}');\")\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 217,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": [
+ "# pd.to_datetime(excess_deaths_upto).strftime('%d %B %Y')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 218,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "uk_covid_deaths.js 100% 25 2.0KB/s 00:00 \n",
+ "uk_deaths_30_days.js 100% 24 1.2KB/s 00:00 \n",
+ "uk_cases_30_days.js 100% 26 21.3KB/s 00:00 \n",
+ "last_uk_date.js 100% 34 2.4KB/s 00:00 \n",
+ "last_intl_date.js 100% 34 3.8KB/s 00:00 \n",
+ "hospital_normalisation_date.js 100% 33 29.1KB/s 00:00 \n"
+ ]
+ }
+ ],
+ "source": [
+ "!scp uk_covid_deaths.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp uk_deaths_30_days.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp uk_cases_30_days.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "# !scp estimated_total_deaths.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "# !scp excess_deaths_upto.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp last_uk_date.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp last_intl_date.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/\n",
+ "!scp hospital_normalisation_date.js neil@ogedei:/var/www/scripts.njae.me.uk/covid/"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "Collapsed": "false"
+ },
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "jupytext": {
+ "formats": "ipynb,md"
+ },
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.8.5"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
projects / covid19.git / blobdiff