{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Incidence du syndrome grippal" ] }, { "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 du syndrome grippal sont disponibles du site Web du [Réseau Sentinelles](http://www.sentiweb.fr/). Nous les récupérons sous forme d'un fichier en format CSV dont chaque ligne correspond à une semaine de la période demandée. Nous téléchargeons toujours le jeu de données complet, qui commence en 1984 et se termine avec une semaine récente." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "data_url = \"http://www.sentiweb.fr/datasets/incidence-PAY-3.csv\"" ] }, { "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": "markdown", "metadata": {}, "source": [ "Afin d'éviter une éventuelle modification du fichier sur le serveur du réseau sentinelle, nous faisons une copie locale du jeu de données. Ainsi les données ne sont téléchargées que si la copie locale n'existe pas." ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Fichier existant\n" ] } ], "source": [ "# Si le fichier csv n'existe pas dans le repertoire local je l'importe de l'url:\n", "import urllib.request\n", "import os\n", "data_file = \"incidence-PAY-3.csv\"\n", "if not os.path.isfile(data_file):\n", " urllib.request.urlretrieve(data_url, data_file)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "raw_data = pd.read_csv(data_file, skiprows=1)\n", "raw_data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Y a-t-il des points manquants dans ce jeux de données ? Oui, la semaine 19 de l'année 1989 n'a pas de valeurs associées." ] }, { "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", "
---|---|---|---|---|---|---|---|---|---|---|
1609 | \n", "198919 | \n", "3 | \n", "0 | \n", "NaN | \n", "NaN | \n", "0 | \n", "NaN | \n", "NaN | \n", "FR | \n", "France | \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", "
---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "202011 | \n", "3 | \n", "101704 | \n", "93652.0 | \n", "109756.0 | \n", "154 | \n", "142.0 | \n", "166.0 | \n", "FR | \n", "France | \n", "
1 | \n", "202010 | \n", "3 | \n", "104977 | \n", "96650.0 | \n", "113304.0 | \n", "159 | \n", "146.0 | \n", "172.0 | \n", "FR | \n", "France | \n", "
2 | \n", "202009 | \n", "3 | \n", "110696 | \n", "102066.0 | \n", "119326.0 | \n", "168 | \n", "155.0 | \n", "181.0 | \n", "FR | \n", "France | \n", "
3 | \n", "202008 | \n", "3 | \n", "143753 | \n", "133984.0 | \n", "153522.0 | \n", "218 | \n", "203.0 | \n", "233.0 | \n", "FR | \n", "France | \n", "
4 | \n", "202007 | \n", "3 | \n", "183610 | \n", "172812.0 | \n", "194408.0 | \n", "279 | \n", "263.0 | \n", "295.0 | \n", "FR | \n", "France | \n", "
5 | \n", "202006 | \n", "3 | \n", "206669 | \n", "195481.0 | \n", "217857.0 | \n", "314 | \n", "297.0 | \n", "331.0 | \n", "FR | \n", "France | \n", "
6 | \n", "202005 | \n", "3 | \n", "187957 | \n", "177445.0 | \n", "198469.0 | \n", "285 | \n", "269.0 | \n", "301.0 | \n", "FR | \n", "France | \n", "
7 | \n", "202004 | \n", "3 | \n", "122331 | \n", "113492.0 | \n", "131170.0 | \n", "186 | \n", "173.0 | \n", "199.0 | \n", "FR | \n", "France | \n", "
8 | \n", "202003 | \n", "3 | \n", "78413 | \n", "71330.0 | \n", "85496.0 | \n", "119 | \n", "108.0 | \n", "130.0 | \n", "FR | \n", "France | \n", "
9 | \n", "202002 | \n", "3 | \n", "53614 | \n", "47654.0 | \n", "59574.0 | \n", "81 | \n", "72.0 | \n", "90.0 | \n", "FR | \n", "France | \n", "
10 | \n", "202001 | \n", "3 | \n", "36850 | \n", "31608.0 | \n", "42092.0 | \n", "56 | \n", "48.0 | \n", "64.0 | \n", "FR | \n", "France | \n", "
11 | \n", "201952 | \n", "3 | \n", "28135 | \n", "23220.0 | \n", "33050.0 | \n", "43 | \n", "36.0 | \n", "50.0 | \n", "FR | \n", "France | \n", "
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13 | \n", "201950 | \n", "3 | \n", "34223 | \n", "29156.0 | \n", "39290.0 | \n", "52 | \n", "44.0 | \n", "60.0 | \n", "FR | \n", "France | \n", "
14 | \n", "201949 | \n", "3 | \n", "25662 | \n", "21414.0 | \n", "29910.0 | \n", "39 | \n", "33.0 | \n", "45.0 | \n", "FR | \n", "France | \n", "
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20 | \n", "201943 | \n", "3 | \n", "9487 | \n", "6448.0 | \n", "12526.0 | \n", "14 | \n", "9.0 | \n", "19.0 | \n", "FR | \n", "France | \n", "
21 | \n", "201942 | \n", "3 | \n", "7747 | \n", "5243.0 | \n", "10251.0 | \n", "12 | \n", "8.0 | \n", "16.0 | \n", "FR | \n", "France | \n", "
22 | \n", "201941 | \n", "3 | \n", "7122 | \n", "4720.0 | \n", "9524.0 | \n", "11 | \n", "7.0 | \n", "15.0 | \n", "FR | \n", "France | \n", "
23 | \n", "201940 | \n", "3 | \n", "8505 | \n", "5784.0 | \n", "11226.0 | \n", "13 | \n", "9.0 | \n", "17.0 | \n", "FR | \n", "France | \n", "
24 | \n", "201939 | \n", "3 | \n", "7091 | \n", "4462.0 | \n", "9720.0 | \n", "11 | \n", "7.0 | \n", "15.0 | \n", "FR | \n", "France | \n", "
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27 | \n", "201936 | \n", "3 | \n", "2295 | \n", "728.0 | \n", "3862.0 | \n", "3 | \n", "1.0 | \n", "5.0 | \n", "FR | \n", "France | \n", "
28 | \n", "201935 | \n", "3 | \n", "1010 | \n", "2.0 | \n", "2018.0 | \n", "2 | \n", "0.0 | \n", "4.0 | \n", "FR | \n", "France | \n", "
29 | \n", "201934 | \n", "3 | \n", "1672 | \n", "279.0 | \n", "3065.0 | \n", "3 | \n", "1.0 | \n", "5.0 | \n", "FR | \n", "France | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
1816 | \n", "198521 | \n", "3 | \n", "26096 | \n", "19621.0 | \n", "32571.0 | \n", "47 | \n", "35.0 | \n", "59.0 | \n", "FR | \n", "France | \n", "
1817 | \n", "198520 | \n", "3 | \n", "27896 | \n", "20885.0 | \n", "34907.0 | \n", "51 | \n", "38.0 | \n", "64.0 | \n", "FR | \n", "France | \n", "
1818 | \n", "198519 | \n", "3 | \n", "43154 | \n", "32821.0 | \n", "53487.0 | \n", "78 | \n", "59.0 | \n", "97.0 | \n", "FR | \n", "France | \n", "
1819 | \n", "198518 | \n", "3 | \n", "40555 | \n", "29935.0 | \n", "51175.0 | \n", "74 | \n", "55.0 | \n", "93.0 | \n", "FR | \n", "France | \n", "
1820 | \n", "198517 | \n", "3 | \n", "34053 | \n", "24366.0 | \n", "43740.0 | \n", "62 | \n", "44.0 | \n", "80.0 | \n", "FR | \n", "France | \n", "
1821 | \n", "198516 | \n", "3 | \n", "50362 | \n", "36451.0 | \n", "64273.0 | \n", "91 | \n", "66.0 | \n", "116.0 | \n", "FR | \n", "France | \n", "
1822 | \n", "198515 | \n", "3 | \n", "63881 | \n", "45538.0 | \n", "82224.0 | \n", "116 | \n", "83.0 | \n", "149.0 | \n", "FR | \n", "France | \n", "
1823 | \n", "198514 | \n", "3 | \n", "134545 | \n", "114400.0 | \n", "154690.0 | \n", "244 | \n", "207.0 | \n", "281.0 | \n", "FR | \n", "France | \n", "
1824 | \n", "198513 | \n", "3 | \n", "197206 | \n", "176080.0 | \n", "218332.0 | \n", "357 | \n", "319.0 | \n", "395.0 | \n", "FR | \n", "France | \n", "
1825 | \n", "198512 | \n", "3 | \n", "245240 | \n", "223304.0 | \n", "267176.0 | \n", "445 | \n", "405.0 | \n", "485.0 | \n", "FR | \n", "France | \n", "
1826 | \n", "198511 | \n", "3 | \n", "276205 | \n", "252399.0 | \n", "300011.0 | \n", "501 | \n", "458.0 | \n", "544.0 | \n", "FR | \n", "France | \n", "
1827 | \n", "198510 | \n", "3 | \n", "353231 | \n", "326279.0 | \n", "380183.0 | \n", "640 | \n", "591.0 | \n", "689.0 | \n", "FR | \n", "France | \n", "
1828 | \n", "198509 | \n", "3 | \n", "369895 | \n", "341109.0 | \n", "398681.0 | \n", "670 | \n", "618.0 | \n", "722.0 | \n", "FR | \n", "France | \n", "
1829 | \n", "198508 | \n", "3 | \n", "389886 | \n", "359529.0 | \n", "420243.0 | \n", "707 | \n", "652.0 | \n", "762.0 | \n", "FR | \n", "France | \n", "
1830 | \n", "198507 | \n", "3 | \n", "471852 | \n", "432599.0 | \n", "511105.0 | \n", "855 | \n", "784.0 | \n", "926.0 | \n", "FR | \n", "France | \n", "
1831 | \n", "198506 | \n", "3 | \n", "565825 | \n", "518011.0 | \n", "613639.0 | \n", "1026 | \n", "939.0 | \n", "1113.0 | \n", "FR | \n", "France | \n", "
1832 | \n", "198505 | \n", "3 | \n", "637302 | \n", "592795.0 | \n", "681809.0 | \n", "1155 | \n", "1074.0 | \n", "1236.0 | \n", "FR | \n", "France | \n", "
1833 | \n", "198504 | \n", "3 | \n", "424937 | \n", "390794.0 | \n", "459080.0 | \n", "770 | \n", "708.0 | \n", "832.0 | \n", "FR | \n", "France | \n", "
1834 | \n", "198503 | \n", "3 | \n", "213901 | \n", "174689.0 | \n", "253113.0 | \n", "388 | \n", "317.0 | \n", "459.0 | \n", "FR | \n", "France | \n", "
1835 | \n", "198502 | \n", "3 | \n", "97586 | \n", "80949.0 | \n", "114223.0 | \n", "177 | \n", "147.0 | \n", "207.0 | \n", "FR | \n", "France | \n", "
1836 | \n", "198501 | \n", "3 | \n", "85489 | \n", "65918.0 | \n", "105060.0 | \n", "155 | \n", "120.0 | \n", "190.0 | \n", "FR | \n", "France | \n", "
1837 | \n", "198452 | \n", "3 | \n", "84830 | \n", "60602.0 | \n", "109058.0 | \n", "154 | \n", "110.0 | \n", "198.0 | \n", "FR | \n", "France | \n", "
1838 | \n", "198451 | \n", "3 | \n", "101726 | \n", "80242.0 | \n", "123210.0 | \n", "185 | \n", "146.0 | \n", "224.0 | \n", "FR | \n", "France | \n", "
1839 | \n", "198450 | \n", "3 | \n", "123680 | \n", "101401.0 | \n", "145959.0 | \n", "225 | \n", "184.0 | \n", "266.0 | \n", "FR | \n", "France | \n", "
1840 | \n", "198449 | \n", "3 | \n", "101073 | \n", "81684.0 | \n", "120462.0 | \n", "184 | \n", "149.0 | \n", "219.0 | \n", "FR | \n", "France | \n", "
1841 | \n", "198448 | \n", "3 | \n", "78620 | \n", "60634.0 | \n", "96606.0 | \n", "143 | \n", "110.0 | \n", "176.0 | \n", "FR | \n", "France | \n", "
1842 | \n", "198447 | \n", "3 | \n", "72029 | \n", "54274.0 | \n", "89784.0 | \n", "131 | \n", "99.0 | \n", "163.0 | \n", "FR | \n", "France | \n", "
1843 | \n", "198446 | \n", "3 | \n", "87330 | \n", "67686.0 | \n", "106974.0 | \n", "159 | \n", "123.0 | \n", "195.0 | \n", "FR | \n", "France | \n", "
1844 | \n", "198445 | \n", "3 | \n", "135223 | \n", "101414.0 | \n", "169032.0 | \n", "246 | \n", "184.0 | \n", "308.0 | \n", "FR | \n", "France | \n", "
1845 | \n", "198444 | \n", "3 | \n", "68422 | \n", "20056.0 | \n", "116788.0 | \n", "125 | \n", "37.0 | \n", "213.0 | \n", "FR | \n", "France | \n", "
1845 rows × 10 columns
\n", "