{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Incidence de la varicelle" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "%matplotlib inline\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import isoweek" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Les données de l'incidence de la varicelle sont disponibles du site Web du Réseau Sentinelles. Nous les récupérons sous forme d'un fichier en format CSV dont chaque ligne correspond à une semaine de la période demandée.\n", "\n", "Il faut passer par les menus \"Surveillance continue\" - \"Base de données\" - \"Accès aux données\" et cliquer sur l'onglet \"Télécharger\", puis choisir les données au format CSV pour la France Métropolitaine." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "data_url = \"http://www.sentiweb.fr/datasets/incidence-PAY-7.csv\"" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Pour des raisons de reproductibilité, nous travaillons sur une copie locale de la base de données. Pour la télécharger, il faut passer par les menus \"Surveillance continue\" - \"Base de données\" - \"Accès aux données\" et cliquer sur l'onglet \"Télécharger\", puis choisir les données au format CSV pour la France Métropolitaine.\n", "\n", "Si la copie locale n'existe pas, nous téléchargeons la base depuis le site web du réseau sentinelle." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "local_data_file = \"LOCAL-incidence-varicelle.csv\"\n", "\n", "import os.path\n", "import urllib.request\n", "if not os.path.exists(local_data_file):\n", " urllib.request.urlretrieve(data_url, local_data_file)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Voici l'explication des colonnes données [sur le site d'origine](https://ns.sentiweb.fr/incidence/csv-schema-v1.json):\n", "\n", "| Nom de colonne | Libellé de colonne |\n", "|----------------|-----------------------------------------------------------------------------------------------------------------------------------|\n", "| week | Semaine calendaire (ISO 8601) |\n", "| indicator | Code de l'indicateur de surveillance |\n", "| inc | Estimation de l'incidence de consultations en nombre de cas |\n", "| inc_low | Estimation de la borne inférieure de l'IC95% du nombre de cas de consultation |\n", "| inc_up | Estimation de la borne supérieure de l'IC95% du nombre de cas de consultation |\n", "| inc100 | Estimation du taux d'incidence du nombre de cas de consultation (en cas pour 100,000 habitants) |\n", "| inc100_low | Estimation de la borne inférieure de l'IC95% du taux d'incidence du nombre de cas de consultation (en cas pour 100,000 habitants) |\n", "| inc100_up | Estimation de la borne supérieure de l'IC95% du taux d'incidence du nombre de cas de consultation (en cas pour 100,000 habitants) |\n", "| geo_insee | Code de la zone géographique concernée (Code INSEE) http://www.insee.fr/fr/methodes/nomenclatures/cog/ |\n", "| geo_name | Libellé de la zone géographique (ce libellé peut être modifié sans préavis) |\n", "\n", "La première ligne du fichier CSV est un commentaire, que nous ignorons en précisant `skiprows=1`." ] }, { "cell_type": "code", "execution_count": 6, "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", "202012 | \n", "7 | \n", "8210 | \n", "5823 | \n", "10597 | \n", "12 | \n", "8 | \n", "16 | \n", "FR | \n", "France | \n", "
1 | \n", "202011 | \n", "7 | \n", "10198 | \n", "7568 | \n", "12828 | \n", "15 | \n", "11 | \n", "19 | \n", "FR | \n", "France | \n", "
2 | \n", "202010 | \n", "7 | \n", "9011 | \n", "6691 | \n", "11331 | \n", "14 | \n", "10 | \n", "18 | \n", "FR | \n", "France | \n", "
3 | \n", "202009 | \n", "7 | \n", "13631 | \n", "10544 | \n", "16718 | \n", "21 | \n", "16 | \n", "26 | \n", "FR | \n", "France | \n", "
4 | \n", "202008 | \n", "7 | \n", "10424 | \n", "7708 | \n", "13140 | \n", "16 | \n", "12 | \n", "20 | \n", "FR | \n", "France | \n", "
5 | \n", "202007 | \n", "7 | \n", "8959 | \n", "6574 | \n", "11344 | \n", "14 | \n", "10 | \n", "18 | \n", "FR | \n", "France | \n", "
6 | \n", "202006 | \n", "7 | \n", "9264 | \n", "6925 | \n", "11603 | \n", "14 | \n", "10 | \n", "18 | \n", "FR | \n", "France | \n", "
7 | \n", "202005 | \n", "7 | \n", "8505 | \n", "6314 | \n", "10696 | \n", "13 | \n", "10 | \n", "16 | \n", "FR | \n", "France | \n", "
8 | \n", "202004 | \n", "7 | \n", "7991 | \n", "5831 | \n", "10151 | \n", "12 | \n", "9 | \n", "15 | \n", "FR | \n", "France | \n", "
9 | \n", "202003 | \n", "7 | \n", "5968 | \n", "4100 | \n", "7836 | \n", "9 | \n", "6 | \n", "12 | \n", "FR | \n", "France | \n", "
10 | \n", "202002 | \n", "7 | \n", "6534 | \n", "4530 | \n", "8538 | \n", "10 | \n", "7 | \n", "13 | \n", "FR | \n", "France | \n", "
11 | \n", "202001 | \n", "7 | \n", "9835 | \n", "7019 | \n", "12651 | \n", "15 | \n", "11 | \n", "19 | \n", "FR | \n", "France | \n", "
12 | \n", "201952 | \n", "7 | \n", "7941 | \n", "5246 | \n", "10636 | \n", "12 | \n", "8 | \n", "16 | \n", "FR | \n", "France | \n", "
13 | \n", "201951 | \n", "7 | \n", "5823 | \n", "3675 | \n", "7971 | \n", "9 | \n", "6 | \n", "12 | \n", "FR | \n", "France | \n", "
14 | \n", "201950 | \n", "7 | \n", "6424 | \n", "4276 | \n", "8572 | \n", "10 | \n", "7 | \n", "13 | \n", "FR | \n", "France | \n", "
15 | \n", "201949 | \n", "7 | \n", "6621 | \n", "4540 | \n", "8702 | \n", "10 | \n", "7 | \n", "13 | \n", "FR | \n", "France | \n", "
16 | \n", "201948 | \n", "7 | \n", "5542 | \n", "3383 | \n", "7701 | \n", "8 | \n", "5 | \n", "11 | \n", "FR | \n", "France | \n", "
17 | \n", "201947 | \n", "7 | \n", "7536 | \n", "5058 | \n", "10014 | \n", "11 | \n", "7 | \n", "15 | \n", "FR | \n", "France | \n", "
18 | \n", "201946 | \n", "7 | \n", "2638 | \n", "1316 | \n", "3960 | \n", "4 | \n", "2 | \n", "6 | \n", "FR | \n", "France | \n", "
19 | \n", "201945 | \n", "7 | \n", "4492 | \n", "2615 | \n", "6369 | \n", "7 | \n", "4 | \n", "10 | \n", "FR | \n", "France | \n", "
20 | \n", "201944 | \n", "7 | \n", "5728 | \n", "3627 | \n", "7829 | \n", "9 | \n", "6 | \n", "12 | \n", "FR | \n", "France | \n", "
21 | \n", "201943 | \n", "7 | \n", "4834 | \n", "2751 | \n", "6917 | \n", "7 | \n", "4 | \n", "10 | \n", "FR | \n", "France | \n", "
22 | \n", "201942 | \n", "7 | \n", "6279 | \n", "3989 | \n", "8569 | \n", "10 | \n", "7 | \n", "13 | \n", "FR | \n", "France | \n", "
23 | \n", "201941 | \n", "7 | \n", "4130 | \n", "2030 | \n", "6230 | \n", "6 | \n", "3 | \n", "9 | \n", "FR | \n", "France | \n", "
24 | \n", "201940 | \n", "7 | \n", "4211 | \n", "2218 | \n", "6204 | \n", "6 | \n", "3 | \n", "9 | \n", "FR | \n", "France | \n", "
25 | \n", "201939 | \n", "7 | \n", "3137 | \n", "1310 | \n", "4964 | \n", "5 | \n", "2 | \n", "8 | \n", "FR | \n", "France | \n", "
26 | \n", "201938 | \n", "7 | \n", "3078 | \n", "1416 | \n", "4740 | \n", "5 | \n", "2 | \n", "8 | \n", "FR | \n", "France | \n", "
27 | \n", "201937 | \n", "7 | \n", "970 | \n", "162 | \n", "1778 | \n", "1 | \n", "0 | \n", "2 | \n", "FR | \n", "France | \n", "
28 | \n", "201936 | \n", "7 | \n", "1277 | \n", "263 | \n", "2291 | \n", "2 | \n", "0 | \n", "4 | \n", "FR | \n", "France | \n", "
29 | \n", "201935 | \n", "7 | \n", "922 | \n", "0 | \n", "1857 | \n", "1 | \n", "0 | \n", "2 | \n", "FR | \n", "France | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
1499 | \n", "199126 | \n", "7 | \n", "17608 | \n", "11304 | \n", "23912 | \n", "31 | \n", "20 | \n", "42 | \n", "FR | \n", "France | \n", "
1500 | \n", "199125 | \n", "7 | \n", "16169 | \n", "10700 | \n", "21638 | \n", "28 | \n", "18 | \n", "38 | \n", "FR | \n", "France | \n", "
1501 | \n", "199124 | \n", "7 | \n", "16171 | \n", "10071 | \n", "22271 | \n", "28 | \n", "17 | \n", "39 | \n", "FR | \n", "France | \n", "
1502 | \n", "199123 | \n", "7 | \n", "11947 | \n", "7671 | \n", "16223 | \n", "21 | \n", "13 | \n", "29 | \n", "FR | \n", "France | \n", "
1503 | \n", "199122 | \n", "7 | \n", "15452 | \n", "9953 | \n", "20951 | \n", "27 | \n", "17 | \n", "37 | \n", "FR | \n", "France | \n", "
1504 | \n", "199121 | \n", "7 | \n", "14903 | \n", "8975 | \n", "20831 | \n", "26 | \n", "16 | \n", "36 | \n", "FR | \n", "France | \n", "
1505 | \n", "199120 | \n", "7 | \n", "19053 | \n", "12742 | \n", "25364 | \n", "34 | \n", "23 | \n", "45 | \n", "FR | \n", "France | \n", "
1506 | \n", "199119 | \n", "7 | \n", "16739 | \n", "11246 | \n", "22232 | \n", "29 | \n", "19 | \n", "39 | \n", "FR | \n", "France | \n", "
1507 | \n", "199118 | \n", "7 | \n", "21385 | \n", "13882 | \n", "28888 | \n", "38 | \n", "25 | \n", "51 | \n", "FR | \n", "France | \n", "
1508 | \n", "199117 | \n", "7 | \n", "13462 | \n", "8877 | \n", "18047 | \n", "24 | \n", "16 | \n", "32 | \n", "FR | \n", "France | \n", "
1509 | \n", "199116 | \n", "7 | \n", "14857 | \n", "10068 | \n", "19646 | \n", "26 | \n", "18 | \n", "34 | \n", "FR | \n", "France | \n", "
1510 | \n", "199115 | \n", "7 | \n", "13975 | \n", "9781 | \n", "18169 | \n", "25 | \n", "18 | \n", "32 | \n", "FR | \n", "France | \n", "
1511 | \n", "199114 | \n", "7 | \n", "12265 | \n", "7684 | \n", "16846 | \n", "22 | \n", "14 | \n", "30 | \n", "FR | \n", "France | \n", "
1512 | \n", "199113 | \n", "7 | \n", "9567 | \n", "6041 | \n", "13093 | \n", "17 | \n", "11 | \n", "23 | \n", "FR | \n", "France | \n", "
1513 | \n", "199112 | \n", "7 | \n", "10864 | \n", "7331 | \n", "14397 | \n", "19 | \n", "13 | \n", "25 | \n", "FR | \n", "France | \n", "
1514 | \n", "199111 | \n", "7 | \n", "15574 | \n", "11184 | \n", "19964 | \n", "27 | \n", "19 | \n", "35 | \n", "FR | \n", "France | \n", "
1515 | \n", "199110 | \n", "7 | \n", "16643 | \n", "11372 | \n", "21914 | \n", "29 | \n", "20 | \n", "38 | \n", "FR | \n", "France | \n", "
1516 | \n", "199109 | \n", "7 | \n", "13741 | \n", "8780 | \n", "18702 | \n", "24 | \n", "15 | \n", "33 | \n", "FR | \n", "France | \n", "
1517 | \n", "199108 | \n", "7 | \n", "13289 | \n", "8813 | \n", "17765 | \n", "23 | \n", "15 | \n", "31 | \n", "FR | \n", "France | \n", "
1518 | \n", "199107 | \n", "7 | \n", "12337 | \n", "8077 | \n", "16597 | \n", "22 | \n", "15 | \n", "29 | \n", "FR | \n", "France | \n", "
1519 | \n", "199106 | \n", "7 | \n", "10877 | \n", "7013 | \n", "14741 | \n", "19 | \n", "12 | \n", "26 | \n", "FR | \n", "France | \n", "
1520 | \n", "199105 | \n", "7 | \n", "10442 | \n", "6544 | \n", "14340 | \n", "18 | \n", "11 | \n", "25 | \n", "FR | \n", "France | \n", "
1521 | \n", "199104 | \n", "7 | \n", "7913 | \n", "4563 | \n", "11263 | \n", "14 | \n", "8 | \n", "20 | \n", "FR | \n", "France | \n", "
1522 | \n", "199103 | \n", "7 | \n", "15387 | \n", "10484 | \n", "20290 | \n", "27 | \n", "18 | \n", "36 | \n", "FR | \n", "France | \n", "
1523 | \n", "199102 | \n", "7 | \n", "16277 | \n", "11046 | \n", "21508 | \n", "29 | \n", "20 | \n", "38 | \n", "FR | \n", "France | \n", "
1524 | \n", "199101 | \n", "7 | \n", "15565 | \n", "10271 | \n", "20859 | \n", "27 | \n", "18 | \n", "36 | \n", "FR | \n", "France | \n", "
1525 | \n", "199052 | \n", "7 | \n", "19375 | \n", "13295 | \n", "25455 | \n", "34 | \n", "23 | \n", "45 | \n", "FR | \n", "France | \n", "
1526 | \n", "199051 | \n", "7 | \n", "19080 | \n", "13807 | \n", "24353 | \n", "34 | \n", "25 | \n", "43 | \n", "FR | \n", "France | \n", "
1527 | \n", "199050 | \n", "7 | \n", "11079 | \n", "6660 | \n", "15498 | \n", "20 | \n", "12 | \n", "28 | \n", "FR | \n", "France | \n", "
1528 | \n", "199049 | \n", "7 | \n", "1143 | \n", "0 | \n", "2610 | \n", "2 | \n", "0 | \n", "5 | \n", "FR | \n", "France | \n", "
1529 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", "
---|