{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Analysis of the incidence of chickenpox" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "%matplotlib inline\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import isoweek" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "The data on the incidence of chickenpox illness are available from the Web site of the [Réseau Sentinelles](http://www.sentiweb.fr/). We download them as a file in CSV format, in which each line corresponds to a week in the observation period." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "data_url = \"https://www.sentiweb.fr/datasets/all/inc-7-PAY.csv\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "It is preferable to first make a copy of the data, and then use that copy in the computational document. To ensure traceability of the data, the computational document must nevertheless contain the URL from which the data was obtained (which we have above). A reader can then download the data again and compare with the version used in the analysis. When publishing a computational document, the copy of the data is published as well, after verifying that republishing the data is legally possible. Below we make the local file with the data if it doesn't yet exist." ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | week | \n", "indicator | \n", "inc | \n", "inc_low | \n", "inc_up | \n", "inc100 | \n", "inc100_low | \n", "inc100_up | \n", "geo_insee | \n", "geo_name | \n", "
---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "202519 | \n", "7 | \n", "4799 | \n", "1358 | \n", "8240 | \n", "7 | \n", "2 | \n", "12 | \n", "FR | \n", "France | \n", "
1 | \n", "202518 | \n", "7 | \n", "4795 | \n", "2500 | \n", "7090 | \n", "7 | \n", "4 | \n", "10 | \n", "FR | \n", "France | \n", "
2 | \n", "202517 | \n", "7 | \n", "6246 | \n", "3424 | \n", "9068 | \n", "9 | \n", "5 | \n", "13 | \n", "FR | \n", "France | \n", "
3 | \n", "202516 | \n", "7 | \n", "6151 | \n", "3193 | \n", "9109 | \n", "9 | \n", "5 | \n", "13 | \n", "FR | \n", "France | \n", "
4 | \n", "202515 | \n", "7 | \n", "5557 | \n", "3262 | \n", "7852 | \n", "8 | \n", "5 | \n", "11 | \n", "FR | \n", "France | \n", "
5 | \n", "202514 | \n", "7 | \n", "4984 | \n", "2858 | \n", "7110 | \n", "7 | \n", "4 | \n", "10 | \n", "FR | \n", "France | \n", "
6 | \n", "202513 | \n", "7 | \n", "5964 | \n", "3608 | \n", "8320 | \n", "9 | \n", "5 | \n", "13 | \n", "FR | \n", "France | \n", "
7 | \n", "202512 | \n", "7 | \n", "3855 | \n", "1995 | \n", "5715 | \n", "6 | \n", "3 | \n", "9 | \n", "FR | \n", "France | \n", "
8 | \n", "202511 | \n", "7 | \n", "5878 | \n", "2747 | \n", "9009 | \n", "9 | \n", "4 | \n", "14 | \n", "FR | \n", "France | \n", "
9 | \n", "202510 | \n", "7 | \n", "2921 | \n", "1421 | \n", "4421 | \n", "4 | \n", "2 | \n", "6 | \n", "FR | \n", "France | \n", "
10 | \n", "202509 | \n", "7 | \n", "3381 | \n", "1468 | \n", "5294 | \n", "5 | \n", "2 | \n", "8 | \n", "FR | \n", "France | \n", "
11 | \n", "202508 | \n", "7 | \n", "2835 | \n", "1286 | \n", "4384 | \n", "4 | \n", "2 | \n", "6 | \n", "FR | \n", "France | \n", "
12 | \n", "202507 | \n", "7 | \n", "4502 | \n", "2382 | \n", "6622 | \n", "7 | \n", "4 | \n", "10 | \n", "FR | \n", "France | \n", "
13 | \n", "202506 | \n", "7 | \n", "3455 | \n", "1958 | \n", "4952 | \n", "5 | \n", "3 | \n", "7 | \n", "FR | \n", "France | \n", "
14 | \n", "202505 | \n", "7 | \n", "2087 | \n", "1056 | \n", "3118 | \n", "3 | \n", "1 | \n", "5 | \n", "FR | \n", "France | \n", "
15 | \n", "202504 | \n", "7 | \n", "6895 | \n", "4466 | \n", "9324 | \n", "10 | \n", "6 | \n", "14 | \n", "FR | \n", "France | \n", "
16 | \n", "202503 | \n", "7 | \n", "2462 | \n", "1161 | \n", "3763 | \n", "4 | \n", "2 | \n", "6 | \n", "FR | \n", "France | \n", "
17 | \n", "202502 | \n", "7 | \n", "5966 | \n", "2757 | \n", "9175 | \n", "9 | \n", "4 | \n", "14 | \n", "FR | \n", "France | \n", "
18 | \n", "202501 | \n", "7 | \n", "6059 | \n", "2451 | \n", "9667 | \n", "9 | \n", "4 | \n", "14 | \n", "FR | \n", "France | \n", "
19 | \n", "202452 | \n", "7 | \n", "4356 | \n", "1776 | \n", "6936 | \n", "7 | \n", "3 | \n", "11 | \n", "FR | \n", "France | \n", "
20 | \n", "202451 | \n", "7 | \n", "4670 | \n", "2239 | \n", "7101 | \n", "7 | \n", "3 | \n", "11 | \n", "FR | \n", "France | \n", "
21 | \n", "202450 | \n", "7 | \n", "7363 | \n", "4438 | \n", "10288 | \n", "11 | \n", "7 | \n", "15 | \n", "FR | \n", "France | \n", "
22 | \n", "202449 | \n", "7 | \n", "6077 | \n", "3631 | \n", "8523 | \n", "9 | \n", "5 | \n", "13 | \n", "FR | \n", "France | \n", "
23 | \n", "202448 | \n", "7 | \n", "4189 | \n", "1454 | \n", "6924 | \n", "6 | \n", "2 | \n", "10 | \n", "FR | \n", "France | \n", "
24 | \n", "202447 | \n", "7 | \n", "1931 | \n", "726 | \n", "3136 | \n", "3 | \n", "1 | \n", "5 | \n", "FR | \n", "France | \n", "
25 | \n", "202446 | \n", "7 | \n", "2260 | \n", "863 | \n", "3657 | \n", "3 | \n", "1 | \n", "5 | \n", "FR | \n", "France | \n", "
26 | \n", "202445 | \n", "7 | \n", "2713 | \n", "1216 | \n", "4210 | \n", "4 | \n", "2 | \n", "6 | \n", "FR | \n", "France | \n", "
27 | \n", "202444 | \n", "7 | \n", "2135 | \n", "676 | \n", "3594 | \n", "3 | \n", "1 | \n", "5 | \n", "FR | \n", "France | \n", "
28 | \n", "202443 | \n", "7 | \n", "2124 | \n", "641 | \n", "3607 | \n", "3 | \n", "1 | \n", "5 | \n", "FR | \n", "France | \n", "
29 | \n", "202442 | \n", "7 | \n", "2621 | \n", "1246 | \n", "3996 | \n", "4 | \n", "2 | \n", "6 | \n", "FR | \n", "France | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
1767 | \n", "199126 | \n", "7 | \n", "17608 | \n", "11304 | \n", "23912 | \n", "31 | \n", "20 | \n", "42 | \n", "FR | \n", "France | \n", "
1768 | \n", "199125 | \n", "7 | \n", "16169 | \n", "10700 | \n", "21638 | \n", "28 | \n", "18 | \n", "38 | \n", "FR | \n", "France | \n", "
1769 | \n", "199124 | \n", "7 | \n", "16171 | \n", "10071 | \n", "22271 | \n", "28 | \n", "17 | \n", "39 | \n", "FR | \n", "France | \n", "
1770 | \n", "199123 | \n", "7 | \n", "11947 | \n", "7671 | \n", "16223 | \n", "21 | \n", "13 | \n", "29 | \n", "FR | \n", "France | \n", "
1771 | \n", "199122 | \n", "7 | \n", "15452 | \n", "9953 | \n", "20951 | \n", "27 | \n", "17 | \n", "37 | \n", "FR | \n", "France | \n", "
1772 | \n", "199121 | \n", "7 | \n", "14903 | \n", "8975 | \n", "20831 | \n", "26 | \n", "16 | \n", "36 | \n", "FR | \n", "France | \n", "
1773 | \n", "199120 | \n", "7 | \n", "19053 | \n", "12742 | \n", "25364 | \n", "34 | \n", "23 | \n", "45 | \n", "FR | \n", "France | \n", "
1774 | \n", "199119 | \n", "7 | \n", "16739 | \n", "11246 | \n", "22232 | \n", "29 | \n", "19 | \n", "39 | \n", "FR | \n", "France | \n", "
1775 | \n", "199118 | \n", "7 | \n", "21385 | \n", "13882 | \n", "28888 | \n", "38 | \n", "25 | \n", "51 | \n", "FR | \n", "France | \n", "
1776 | \n", "199117 | \n", "7 | \n", "13462 | \n", "8877 | \n", "18047 | \n", "24 | \n", "16 | \n", "32 | \n", "FR | \n", "France | \n", "
1777 | \n", "199116 | \n", "7 | \n", "14857 | \n", "10068 | \n", "19646 | \n", "26 | \n", "18 | \n", "34 | \n", "FR | \n", "France | \n", "
1778 | \n", "199115 | \n", "7 | \n", "13975 | \n", "9781 | \n", "18169 | \n", "25 | \n", "18 | \n", "32 | \n", "FR | \n", "France | \n", "
1779 | \n", "199114 | \n", "7 | \n", "12265 | \n", "7684 | \n", "16846 | \n", "22 | \n", "14 | \n", "30 | \n", "FR | \n", "France | \n", "
1780 | \n", "199113 | \n", "7 | \n", "9567 | \n", "6041 | \n", "13093 | \n", "17 | \n", "11 | \n", "23 | \n", "FR | \n", "France | \n", "
1781 | \n", "199112 | \n", "7 | \n", "10864 | \n", "7331 | \n", "14397 | \n", "19 | \n", "13 | \n", "25 | \n", "FR | \n", "France | \n", "
1782 | \n", "199111 | \n", "7 | \n", "15574 | \n", "11184 | \n", "19964 | \n", "27 | \n", "19 | \n", "35 | \n", "FR | \n", "France | \n", "
1783 | \n", "199110 | \n", "7 | \n", "16643 | \n", "11372 | \n", "21914 | \n", "29 | \n", "20 | \n", "38 | \n", "FR | \n", "France | \n", "
1784 | \n", "199109 | \n", "7 | \n", "13741 | \n", "8780 | \n", "18702 | \n", "24 | \n", "15 | \n", "33 | \n", "FR | \n", "France | \n", "
1785 | \n", "199108 | \n", "7 | \n", "13289 | \n", "8813 | \n", "17765 | \n", "23 | \n", "15 | \n", "31 | \n", "FR | \n", "France | \n", "
1786 | \n", "199107 | \n", "7 | \n", "12337 | \n", "8077 | \n", "16597 | \n", "22 | \n", "15 | \n", "29 | \n", "FR | \n", "France | \n", "
1787 | \n", "199106 | \n", "7 | \n", "10877 | \n", "7013 | \n", "14741 | \n", "19 | \n", "12 | \n", "26 | \n", "FR | \n", "France | \n", "
1788 | \n", "199105 | \n", "7 | \n", "10442 | \n", "6544 | \n", "14340 | \n", "18 | \n", "11 | \n", "25 | \n", "FR | \n", "France | \n", "
1789 | \n", "199104 | \n", "7 | \n", "7913 | \n", "4563 | \n", "11263 | \n", "14 | \n", "8 | \n", "20 | \n", "FR | \n", "France | \n", "
1790 | \n", "199103 | \n", "7 | \n", "15387 | \n", "10484 | \n", "20290 | \n", "27 | \n", "18 | \n", "36 | \n", "FR | \n", "France | \n", "
1791 | \n", "199102 | \n", "7 | \n", "16277 | \n", "11046 | \n", "21508 | \n", "29 | \n", "20 | \n", "38 | \n", "FR | \n", "France | \n", "
1792 | \n", "199101 | \n", "7 | \n", "15565 | \n", "10271 | \n", "20859 | \n", "27 | \n", "18 | \n", "36 | \n", "FR | \n", "France | \n", "
1793 | \n", "199052 | \n", "7 | \n", "19375 | \n", "13295 | \n", "25455 | \n", "34 | \n", "23 | \n", "45 | \n", "FR | \n", "France | \n", "
1794 | \n", "199051 | \n", "7 | \n", "19080 | \n", "13807 | \n", "24353 | \n", "34 | \n", "25 | \n", "43 | \n", "FR | \n", "France | \n", "
1795 | \n", "199050 | \n", "7 | \n", "11079 | \n", "6660 | \n", "15498 | \n", "20 | \n", "12 | \n", "28 | \n", "FR | \n", "France | \n", "
1796 | \n", "199049 | \n", "7 | \n", "1143 | \n", "0 | \n", "2610 | \n", "2 | \n", "0 | \n", "5 | \n", "FR | \n", "France | \n", "
1797 rows × 10 columns
\n", "\n", " | week | \n", "indicator | \n", "inc | \n", "inc_low | \n", "inc_up | \n", "inc100 | \n", "inc100_low | \n", "inc100_up | \n", "geo_insee | \n", "geo_name | \n", "
---|