{ "cells": [ { "cell_type": "code", "execution_count": 77, "metadata": { "Collapsed": "false" }, "outputs": [], "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", "import matplotlib.animation as ani\n", "%matplotlib inline" ] }, { "cell_type": "markdown", "metadata": { "Collapsed": "false" }, "source": [ "Belgian data from https://epistat.wiv-isp.be/covid/" ] }, { "cell_type": "code", "execution_count": 78, "metadata": { "Collapsed": "false" }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " % Total % Received % Xferd Average Speed Time Time Time Current\n", " Dload Upload Total Spent Left Speed\n", "100 126k 100 126k 0 0 337k 0 --:--:-- --:--:-- --:--:-- 337k\n" ] } ], "source": [ "!curl \"https://epistat.sciensano.be/Data/COVID19BE_tests.csv\" > COVID19BE_tests.csv" ] }, { "cell_type": "code", "execution_count": 79, "metadata": { "Collapsed": "false" }, "outputs": [], "source": [ "raw_data = pd.read_csv('COVID19BE_tests.csv', \n", " parse_dates=[0], dayfirst=True,\n", " keep_default_na=False, na_values = ['']\n", " )" ] }, { "cell_type": "code", "execution_count": 80, "metadata": { "Collapsed": "false" }, "outputs": [ { "data": { "text/plain": [ "DATE datetime64[ns]\n", "PROVINCE object\n", "REGION object\n", "TESTS_ALL int64\n", "TESTS_ALL_POS int64\n", "dtype: object" ] }, "execution_count": 80, "metadata": {}, "output_type": "execute_result" } ], "source": [ "raw_data.dtypes" ] }, { "cell_type": "code", "execution_count": 81, "metadata": { "Collapsed": "false" }, "outputs": [ { "data": { "text/html": [ "
\n", " | TESTS_ALL | \n", "TESTS_ALL_POS | \n", "
---|---|---|
DATE | \n", "\n", " | \n", " |
2020-03-01 | \n", "82 | \n", "0 | \n", "
2020-03-02 | \n", "317 | \n", "10 | \n", "
2020-03-03 | \n", "538 | \n", "21 | \n", "
2020-03-04 | \n", "701 | \n", "37 | \n", "
2020-03-05 | \n", "773 | \n", "65 | \n", "
... | \n", "... | \n", "... | \n", "
2020-11-08 | \n", "13284 | \n", "2785 | \n", "
2020-11-09 | \n", "21947 | \n", "4480 | \n", "
2020-11-10 | \n", "38400 | \n", "8086 | \n", "
2020-11-11 | \n", "31388 | \n", "6091 | \n", "
2020-11-12 | \n", "26443 | \n", "4665 | \n", "
257 rows × 2 columns
\n", "\n", " | cases | \n", "deaths | \n", "cases_culm | \n", "deaths_culm | \n", "cases_diff | \n", "deaths_diff | \n", "cases_m7 | \n", "deaths_m7 | \n", "deaths_g4 | \n", "deaths_g7 | \n", "doubling_time | \n", "doubling_time_7 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
dateRep | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
2019-12-31 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "NaN | \n", "NaN | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
2020-01-01 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0.0 | \n", "0.0 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
2020-01-02 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0.0 | \n", "0.0 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
2020-01-03 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0.0 | \n", "0.0 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
2020-01-04 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0.0 | \n", "0.0 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "0.000000 | \n", "NaN | \n", "NaN | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
2020-11-10 | \n", "8320 | \n", "189 | \n", "513491 | \n", "13591 | \n", "6875.0 | \n", "-16.0 | \n", "6909.571429 | \n", "196.571429 | \n", "203.540082 | \n", "196.032323 | \n", "46.629293 | \n", "48.401920 | \n", "
2020-11-11 | \n", "7217 | \n", "199 | \n", "520708 | \n", "13790 | \n", "-1103.0 | \n", "10.0 | \n", "6213.285714 | \n", "201.000000 | \n", "199.875596 | \n", "200.832476 | \n", "48.167987 | \n", "47.940131 | \n", "
2020-11-12 | \n", "1819 | \n", "177 | \n", "522527 | \n", "13967 | \n", "-5398.0 | \n", "-22.0 | \n", "5158.571429 | \n", "199.000000 | \n", "192.203150 | \n", "198.660293 | \n", "50.715337 | \n", "49.078127 | \n", "
2020-11-13 | \n", "2385 | \n", "124 | \n", "524912 | \n", "14091 | \n", "566.0 | \n", "-53.0 | \n", "4407.142857 | \n", "187.857143 | \n", "169.503027 | \n", "185.282927 | \n", "57.968081 | \n", "53.060535 | \n", "
2020-11-14 | \n", "4 | \n", "15 | \n", "524916 | \n", "14106 | \n", "-2381.0 | \n", "-109.0 | \n", "3459.571429 | \n", "159.428571 | \n", "89.967328 | \n", "126.745394 | \n", "109.024927 | \n", "77.489169 | \n", "
320 rows × 12 columns
\n", "\n", " | cases | \n", "deaths | \n", "cases_culm | \n", "deaths_culm | \n", "cases_diff | \n", "deaths_diff | \n", "cases_m7 | \n", "deaths_m7 | \n", "deaths_g4 | \n", "deaths_g7 | \n", "doubling_time | \n", "doubling_time_7 | \n", "TESTS_ALL | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2020-03-10 | \n", "94 | \n", "1 | \n", "501 | \n", "1 | \n", "30.0 | \n", "1.0 | \n", "66.142857 | \n", "0.142857 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "804.0 | \n", "
2020-03-11 | \n", "99 | \n", "0 | \n", "600 | \n", "1 | \n", "5.0 | \n", "-1.0 | \n", "75.428571 | \n", "0.142857 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "1108.0 | \n", "
2020-03-12 | \n", "174 | \n", "3 | \n", "774 | \n", "4 | \n", "75.0 | \n", "3.0 | \n", "92.714286 | \n", "0.571429 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "1438.0 | \n", "
2020-03-13 | \n", "250 | \n", "1 | \n", "1024 | \n", "5 | \n", "76.0 | \n", "-2.0 | \n", "116.857143 | \n", "0.714286 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "2524.0 | \n", "
2020-03-14 | \n", "338 | \n", "3 | \n", "1362 | \n", "8 | \n", "88.0 | \n", "2.0 | \n", "149.428571 | \n", "1.142857 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "2171.0 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
2020-11-08 | \n", "3027 | \n", "207 | \n", "503726 | \n", "13197 | \n", "-3610.0 | \n", "-7.0 | \n", "7873.571429 | \n", "192.428571 | \n", "203.325671 | \n", "191.422569 | \n", "45.334910 | \n", "48.132496 | \n", "13284.0 | \n", "
2020-11-09 | \n", "1445 | \n", "205 | \n", "505171 | \n", "13402 | \n", "-1582.0 | \n", "-2.0 | \n", "7699.285714 | \n", "198.857143 | \n", "206.953291 | \n", "198.321322 | \n", "45.232911 | \n", "47.186672 | \n", "21947.0 | \n", "
2020-11-10 | \n", "8320 | \n", "189 | \n", "513491 | \n", "13591 | \n", "6875.0 | \n", "-16.0 | \n", "6909.571429 | \n", "196.571429 | \n", "203.540082 | \n", "196.032323 | \n", "46.629293 | \n", "48.401920 | \n", "38400.0 | \n", "
2020-11-11 | \n", "7217 | \n", "199 | \n", "520708 | \n", "13790 | \n", "-1103.0 | \n", "10.0 | \n", "6213.285714 | \n", "201.000000 | \n", "199.875596 | \n", "200.832476 | \n", "48.167987 | \n", "47.940131 | \n", "31388.0 | \n", "
2020-11-12 | \n", "1819 | \n", "177 | \n", "522527 | \n", "13967 | \n", "-5398.0 | \n", "-22.0 | \n", "5158.571429 | \n", "199.000000 | \n", "192.203150 | \n", "198.660293 | \n", "50.715337 | \n", "49.078127 | \n", "26443.0 | \n", "
248 rows × 13 columns
\n", "\n", " | cases | \n", "deaths | \n", "cases_culm | \n", "deaths_culm | \n", "cases_diff | \n", "deaths_diff | \n", "cases_m7 | \n", "deaths_m7 | \n", "deaths_g4 | \n", "deaths_g7 | \n", "doubling_time | \n", "doubling_time_7 | \n", "TESTS_ALL | \n", "tests_m7 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2020-03-10 | \n", "94 | \n", "1 | \n", "501 | \n", "1 | \n", "30.0 | \n", "1.0 | \n", "94.000000 | \n", "1.000000 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "804.0 | \n", "804.000000 | \n", "
2020-03-11 | \n", "99 | \n", "0 | \n", "600 | \n", "1 | \n", "5.0 | \n", "-1.0 | \n", "96.500000 | \n", "0.500000 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "1108.0 | \n", "956.000000 | \n", "
2020-03-12 | \n", "174 | \n", "3 | \n", "774 | \n", "4 | \n", "75.0 | \n", "3.0 | \n", "122.333333 | \n", "1.333333 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "1438.0 | \n", "1116.666667 | \n", "
2020-03-13 | \n", "250 | \n", "1 | \n", "1024 | \n", "5 | \n", "76.0 | \n", "-2.0 | \n", "154.250000 | \n", "1.250000 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "2524.0 | \n", "1468.500000 | \n", "
2020-03-14 | \n", "338 | \n", "3 | \n", "1362 | \n", "8 | \n", "88.0 | \n", "2.0 | \n", "191.000000 | \n", "1.600000 | \n", "0.000000 | \n", "0.000000 | \n", "inf | \n", "inf | \n", "2171.0 | \n", "1609.000000 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
2020-11-08 | \n", "3027 | \n", "207 | \n", "503726 | \n", "13197 | \n", "-3610.0 | \n", "-7.0 | \n", "7873.571429 | \n", "192.428571 | \n", "203.325671 | \n", "191.422569 | \n", "45.334910 | \n", "48.132496 | \n", "13284.0 | \n", "36906.000000 | \n", "
2020-11-09 | \n", "1445 | \n", "205 | \n", "505171 | \n", "13402 | \n", "-1582.0 | \n", "-2.0 | \n", "7699.285714 | \n", "198.857143 | \n", "206.953291 | \n", "198.321322 | \n", "45.232911 | \n", "47.186672 | \n", "21947.0 | \n", "35916.142857 | \n", "
2020-11-10 | \n", "8320 | \n", "189 | \n", "513491 | \n", "13591 | \n", "6875.0 | \n", "-16.0 | \n", "6909.571429 | \n", "196.571429 | \n", "203.540082 | \n", "196.032323 | \n", "46.629293 | \n", "48.401920 | \n", "38400.0 | \n", "33588.857143 | \n", "
2020-11-11 | \n", "7217 | \n", "199 | \n", "520708 | \n", "13790 | \n", "-1103.0 | \n", "10.0 | \n", "6213.285714 | \n", "201.000000 | \n", "199.875596 | \n", "200.832476 | \n", "48.167987 | \n", "47.940131 | \n", "31388.0 | \n", "31691.428571 | \n", "
2020-11-12 | \n", "1819 | \n", "177 | \n", "522527 | \n", "13967 | \n", "-5398.0 | \n", "-22.0 | \n", "5158.571429 | \n", "199.000000 | \n", "192.203150 | \n", "198.660293 | \n", "50.715337 | \n", "49.078127 | \n", "26443.0 | \n", "28969.857143 | \n", "
248 rows × 14 columns
\n", "\n", " | cases | \n", "deaths | \n", "cases_culm | \n", "deaths_culm | \n", "cases_diff | \n", "deaths_diff | \n", "cases_m7 | \n", "deaths_m7 | \n", "deaths_g4 | \n", "deaths_g7 | \n", "doubling_time | \n", "doubling_time_7 | \n", "TESTS_ALL | \n", "tests_m7 | \n", "fraction_positive | \n", "fraction_positive_m7 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
2020-06-15 | \n", "22 | \n", "3 | \n", "60484 | \n", "9547 | \n", "-27.0 | \n", "-2.0 | \n", "95.857143 | \n", "8.285714 | \n", "5.692425 | \n", "7.520666 | \n", "1162.852153 | \n", "880.252074 | \n", "11905.0 | \n", "12538.000000 | \n", "0.001848 | \n", "0.007645 | \n", "
2020-06-16 | \n", "147 | \n", "8 | \n", "60631 | \n", "9555 | \n", "125.0 | \n", "5.0 | \n", "95.142857 | \n", "8.142857 | \n", "5.885662 | \n", "7.395181 | \n", "1125.627162 | \n", "895.932593 | \n", "15194.0 | \n", "12553.571429 | \n", "0.009675 | \n", "0.007579 | \n", "