{ "cells": [ { "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": [ "Les données de l'incidence de la varicelle 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": 2, "metadata": {}, "outputs": [], "source": [ "data_url = \"https://www.sentiweb.fr/datasets/incidence-PAY-7.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": [ "Essaye d'importer les données depuis un fichier local afin de péréniser les données en cas de problème avec la source.\n", "Si le fichier local n'existe pas, importe les données depuis le site internet original." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "imported local data\n", " Unnamed: 0 week indicator inc inc_low inc_up inc100 \\\n", "0 0 202113 7 9838 6381 13295 15 \n", "1 1 202112 7 11520 8415 14625 17 \n", "2 2 202111 7 9386 6678 12094 14 \n", "3 3 202110 7 9056 6452 11660 14 \n", "4 4 202109 7 10988 7938 14038 17 \n", "5 5 202108 7 11281 8361 14201 17 \n", "6 6 202107 7 13561 10315 16807 21 \n", "7 7 202106 7 13401 9810 16992 20 \n", "8 8 202105 7 12210 8988 15432 18 \n", "9 9 202104 7 12026 8826 15226 18 \n", "10 10 202103 7 8913 6375 11451 13 \n", "11 11 202102 7 7795 5430 10160 12 \n", "12 12 202101 7 10525 7750 13300 16 \n", "13 13 202053 7 11978 8406 15550 18 \n", "14 14 202052 7 12012 8285 15739 18 \n", "15 15 202051 7 10564 7574 13554 16 \n", "16 16 202050 7 7063 4744 9382 11 \n", "17 17 202049 7 5026 3145 6907 8 \n", "18 18 202048 7 6683 4312 9054 10 \n", "19 19 202047 7 4999 2963 7035 8 \n", "20 20 202046 7 3752 1963 5541 6 \n", "21 21 202045 7 3696 2016 5376 6 \n", "22 22 202044 7 4391 2375 6407 7 \n", "23 23 202043 7 4376 2505 6247 7 \n", "24 24 202042 7 4000 1979 6021 6 \n", "25 25 202041 7 3961 2099 5823 6 \n", "26 26 202040 7 2078 675 3481 3 \n", "27 27 202039 7 1049 237 1861 2 \n", "28 28 202038 7 2251 781 3721 3 \n", "29 29 202037 7 1584 405 2763 2 \n", "... ... ... ... ... ... ... ... \n", "1553 1553 199126 7 17608 11304 23912 31 \n", "1554 1554 199125 7 16169 10700 21638 28 \n", "1555 1555 199124 7 16171 10071 22271 28 \n", "1556 1556 199123 7 11947 7671 16223 21 \n", "1557 1557 199122 7 15452 9953 20951 27 \n", "1558 1558 199121 7 14903 8975 20831 26 \n", "1559 1559 199120 7 19053 12742 25364 34 \n", "1560 1560 199119 7 16739 11246 22232 29 \n", "1561 1561 199118 7 21385 13882 28888 38 \n", "1562 1562 199117 7 13462 8877 18047 24 \n", "1563 1563 199116 7 14857 10068 19646 26 \n", "1564 1564 199115 7 13975 9781 18169 25 \n", "1565 1565 199114 7 12265 7684 16846 22 \n", "1566 1566 199113 7 9567 6041 13093 17 \n", "1567 1567 199112 7 10864 7331 14397 19 \n", "1568 1568 199111 7 15574 11184 19964 27 \n", "1569 1569 199110 7 16643 11372 21914 29 \n", "1570 1570 199109 7 13741 8780 18702 24 \n", "1571 1571 199108 7 13289 8813 17765 23 \n", "1572 1572 199107 7 12337 8077 16597 22 \n", "1573 1573 199106 7 10877 7013 14741 19 \n", "1574 1574 199105 7 10442 6544 14340 18 \n", "1575 1575 199104 7 7913 4563 11263 14 \n", "1576 1576 199103 7 15387 10484 20290 27 \n", "1577 1577 199102 7 16277 11046 21508 29 \n", "1578 1578 199101 7 15565 10271 20859 27 \n", "1579 1579 199052 7 19375 13295 25455 34 \n", "1580 1580 199051 7 19080 13807 24353 34 \n", "1581 1581 199050 7 11079 6660 15498 20 \n", "1582 1582 199049 7 1143 0 2610 2 \n", "\n", " inc100_low inc100_up geo_insee geo_name \n", "0 10 20 FR France \n", "1 12 22 FR France \n", "2 10 18 FR France \n", "3 10 18 FR France \n", "4 12 22 FR France \n", "5 13 21 FR France \n", "6 16 26 FR France \n", "7 15 25 FR France \n", "8 13 23 FR France \n", "9 13 23 FR France \n", "10 9 17 FR France \n", "11 8 16 FR France \n", "12 12 20 FR France \n", "13 13 23 FR France \n", "14 12 24 FR France \n", "15 11 21 FR France \n", "16 7 15 FR France \n", "17 5 11 FR France \n", "18 6 14 FR France \n", "19 5 11 FR France \n", "20 3 9 FR France \n", "21 3 9 FR France \n", "22 4 10 FR France \n", "23 4 10 FR France \n", "24 3 9 FR France \n", "25 3 9 FR France \n", "26 1 5 FR France \n", "27 1 3 FR France \n", "28 1 5 FR France \n", "29 0 4 FR France \n", "... ... ... ... ... \n", "1553 20 42 FR France \n", "1554 18 38 FR France \n", "1555 17 39 FR France \n", "1556 13 29 FR France \n", "1557 17 37 FR France \n", "1558 16 36 FR France \n", "1559 23 45 FR France \n", "1560 19 39 FR France \n", "1561 25 51 FR France \n", "1562 16 32 FR France \n", "1563 18 34 FR France \n", "1564 18 32 FR France \n", "1565 14 30 FR France \n", "1566 11 23 FR France \n", "1567 13 25 FR France \n", "1568 19 35 FR France \n", "1569 20 38 FR France \n", "1570 15 33 FR France \n", "1571 15 31 FR France \n", "1572 15 29 FR France \n", "1573 12 26 FR France \n", "1574 11 25 FR France \n", "1575 8 20 FR France \n", "1576 18 36 FR France \n", "1577 20 38 FR France \n", "1578 18 36 FR France \n", "1579 23 45 FR France \n", "1580 25 43 FR France \n", "1581 12 28 FR France \n", "1582 0 5 FR France \n", "\n", "[1583 rows x 11 columns]\n" ] } ], "source": [ "try:\n", " raw_data = pd.read_csv('incidence-PAY-7.csv')\n", " print(\"imported local data\")\n", "except FileNotFoundError:\n", " print(\"import data from the internet and save it to a local file\")\n", " raw_data = pd.read_csv(data_url, skiprows=1)\n", " raw_data.to_csv('incidence-PAY-7.csv')\n", " \n", "print(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": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | Unnamed: 0 | \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", "
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11 | \n", "11 | \n", "202102 | \n", "7 | \n", "7795 | \n", "5430 | \n", "10160 | \n", "12 | \n", "8 | \n", "16 | \n", "FR | \n", "France | \n", "
12 | \n", "12 | \n", "202101 | \n", "7 | \n", "10525 | \n", "7750 | \n", "13300 | \n", "16 | \n", "12 | \n", "20 | \n", "FR | \n", "France | \n", "
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14 | \n", "14 | \n", "202052 | \n", "7 | \n", "12012 | \n", "8285 | \n", "15739 | \n", "18 | \n", "12 | \n", "24 | \n", "FR | \n", "France | \n", "
15 | \n", "15 | \n", "202051 | \n", "7 | \n", "10564 | \n", "7574 | \n", "13554 | \n", "16 | \n", "11 | \n", "21 | \n", "FR | \n", "France | \n", "
16 | \n", "16 | \n", "202050 | \n", "7 | \n", "7063 | \n", "4744 | \n", "9382 | \n", "11 | \n", "7 | \n", "15 | \n", "FR | \n", "France | \n", "
17 | \n", "17 | \n", "202049 | \n", "7 | \n", "5026 | \n", "3145 | \n", "6907 | \n", "8 | \n", "5 | \n", "11 | \n", "FR | \n", "France | \n", "
18 | \n", "18 | \n", "202048 | \n", "7 | \n", "6683 | \n", "4312 | \n", "9054 | \n", "10 | \n", "6 | \n", "14 | \n", "FR | \n", "France | \n", "
19 | \n", "19 | \n", "202047 | \n", "7 | \n", "4999 | \n", "2963 | \n", "7035 | \n", "8 | \n", "5 | \n", "11 | \n", "FR | \n", "France | \n", "
20 | \n", "20 | \n", "202046 | \n", "7 | \n", "3752 | \n", "1963 | \n", "5541 | \n", "6 | \n", "3 | \n", "9 | \n", "FR | \n", "France | \n", "
21 | \n", "21 | \n", "202045 | \n", "7 | \n", "3696 | \n", "2016 | \n", "5376 | \n", "6 | \n", "3 | \n", "9 | \n", "FR | \n", "France | \n", "
22 | \n", "22 | \n", "202044 | \n", "7 | \n", "4391 | \n", "2375 | \n", "6407 | \n", "7 | \n", "4 | \n", "10 | \n", "FR | \n", "France | \n", "
23 | \n", "23 | \n", "202043 | \n", "7 | \n", "4376 | \n", "2505 | \n", "6247 | \n", "7 | \n", "4 | \n", "10 | \n", "FR | \n", "France | \n", "
24 | \n", "24 | \n", "202042 | \n", "7 | \n", "4000 | \n", "1979 | \n", "6021 | \n", "6 | \n", "3 | \n", "9 | \n", "FR | \n", "France | \n", "
25 | \n", "25 | \n", "202041 | \n", "7 | \n", "3961 | \n", "2099 | \n", "5823 | \n", "6 | \n", "3 | \n", "9 | \n", "FR | \n", "France | \n", "
26 | \n", "26 | \n", "202040 | \n", "7 | \n", "2078 | \n", "675 | \n", "3481 | \n", "3 | \n", "1 | \n", "5 | \n", "FR | \n", "France | \n", "
27 | \n", "27 | \n", "202039 | \n", "7 | \n", "1049 | \n", "237 | \n", "1861 | \n", "2 | \n", "1 | \n", "3 | \n", "FR | \n", "France | \n", "
28 | \n", "28 | \n", "202038 | \n", "7 | \n", "2251 | \n", "781 | \n", "3721 | \n", "3 | \n", "1 | \n", "5 | \n", "FR | \n", "France | \n", "
29 | \n", "29 | \n", "202037 | \n", "7 | \n", "1584 | \n", "405 | \n", "2763 | \n", "2 | \n", "0 | \n", "4 | \n", "FR | \n", "France | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
1553 | \n", "1553 | \n", "199126 | \n", "7 | \n", "17608 | \n", "11304 | \n", "23912 | \n", "31 | \n", "20 | \n", "42 | \n", "FR | \n", "France | \n", "
1554 | \n", "1554 | \n", "199125 | \n", "7 | \n", "16169 | \n", "10700 | \n", "21638 | \n", "28 | \n", "18 | \n", "38 | \n", "FR | \n", "France | \n", "
1555 | \n", "1555 | \n", "199124 | \n", "7 | \n", "16171 | \n", "10071 | \n", "22271 | \n", "28 | \n", "17 | \n", "39 | \n", "FR | \n", "France | \n", "
1556 | \n", "1556 | \n", "199123 | \n", "7 | \n", "11947 | \n", "7671 | \n", "16223 | \n", "21 | \n", "13 | \n", "29 | \n", "FR | \n", "France | \n", "
1557 | \n", "1557 | \n", "199122 | \n", "7 | \n", "15452 | \n", "9953 | \n", "20951 | \n", "27 | \n", "17 | \n", "37 | \n", "FR | \n", "France | \n", "
1558 | \n", "1558 | \n", "199121 | \n", "7 | \n", "14903 | \n", "8975 | \n", "20831 | \n", "26 | \n", "16 | \n", "36 | \n", "FR | \n", "France | \n", "
1559 | \n", "1559 | \n", "199120 | \n", "7 | \n", "19053 | \n", "12742 | \n", "25364 | \n", "34 | \n", "23 | \n", "45 | \n", "FR | \n", "France | \n", "
1560 | \n", "1560 | \n", "199119 | \n", "7 | \n", "16739 | \n", "11246 | \n", "22232 | \n", "29 | \n", "19 | \n", "39 | \n", "FR | \n", "France | \n", "
1561 | \n", "1561 | \n", "199118 | \n", "7 | \n", "21385 | \n", "13882 | \n", "28888 | \n", "38 | \n", "25 | \n", "51 | \n", "FR | \n", "France | \n", "
1562 | \n", "1562 | \n", "199117 | \n", "7 | \n", "13462 | \n", "8877 | \n", "18047 | \n", "24 | \n", "16 | \n", "32 | \n", "FR | \n", "France | \n", "
1563 | \n", "1563 | \n", "199116 | \n", "7 | \n", "14857 | \n", "10068 | \n", "19646 | \n", "26 | \n", "18 | \n", "34 | \n", "FR | \n", "France | \n", "
1564 | \n", "1564 | \n", "199115 | \n", "7 | \n", "13975 | \n", "9781 | \n", "18169 | \n", "25 | \n", "18 | \n", "32 | \n", "FR | \n", "France | \n", "
1565 | \n", "1565 | \n", "199114 | \n", "7 | \n", "12265 | \n", "7684 | \n", "16846 | \n", "22 | \n", "14 | \n", "30 | \n", "FR | \n", "France | \n", "
1566 | \n", "1566 | \n", "199113 | \n", "7 | \n", "9567 | \n", "6041 | \n", "13093 | \n", "17 | \n", "11 | \n", "23 | \n", "FR | \n", "France | \n", "
1567 | \n", "1567 | \n", "199112 | \n", "7 | \n", "10864 | \n", "7331 | \n", "14397 | \n", "19 | \n", "13 | \n", "25 | \n", "FR | \n", "France | \n", "
1568 | \n", "1568 | \n", "199111 | \n", "7 | \n", "15574 | \n", "11184 | \n", "19964 | \n", "27 | \n", "19 | \n", "35 | \n", "FR | \n", "France | \n", "
1569 | \n", "1569 | \n", "199110 | \n", "7 | \n", "16643 | \n", "11372 | \n", "21914 | \n", "29 | \n", "20 | \n", "38 | \n", "FR | \n", "France | \n", "
1570 | \n", "1570 | \n", "199109 | \n", "7 | \n", "13741 | \n", "8780 | \n", "18702 | \n", "24 | \n", "15 | \n", "33 | \n", "FR | \n", "France | \n", "
1571 | \n", "1571 | \n", "199108 | \n", "7 | \n", "13289 | \n", "8813 | \n", "17765 | \n", "23 | \n", "15 | \n", "31 | \n", "FR | \n", "France | \n", "
1572 | \n", "1572 | \n", "199107 | \n", "7 | \n", "12337 | \n", "8077 | \n", "16597 | \n", "22 | \n", "15 | \n", "29 | \n", "FR | \n", "France | \n", "
1573 | \n", "1573 | \n", "199106 | \n", "7 | \n", "10877 | \n", "7013 | \n", "14741 | \n", "19 | \n", "12 | \n", "26 | \n", "FR | \n", "France | \n", "
1574 | \n", "1574 | \n", "199105 | \n", "7 | \n", "10442 | \n", "6544 | \n", "14340 | \n", "18 | \n", "11 | \n", "25 | \n", "FR | \n", "France | \n", "
1575 | \n", "1575 | \n", "199104 | \n", "7 | \n", "7913 | \n", "4563 | \n", "11263 | \n", "14 | \n", "8 | \n", "20 | \n", "FR | \n", "France | \n", "
1576 | \n", "1576 | \n", "199103 | \n", "7 | \n", "15387 | \n", "10484 | \n", "20290 | \n", "27 | \n", "18 | \n", "36 | \n", "FR | \n", "France | \n", "
1577 | \n", "1577 | \n", "199102 | \n", "7 | \n", "16277 | \n", "11046 | \n", "21508 | \n", "29 | \n", "20 | \n", "38 | \n", "FR | \n", "France | \n", "
1578 | \n", "1578 | \n", "199101 | \n", "7 | \n", "15565 | \n", "10271 | \n", "20859 | \n", "27 | \n", "18 | \n", "36 | \n", "FR | \n", "France | \n", "
1579 | \n", "1579 | \n", "199052 | \n", "7 | \n", "19375 | \n", "13295 | \n", "25455 | \n", "34 | \n", "23 | \n", "45 | \n", "FR | \n", "France | \n", "
1580 | \n", "1580 | \n", "199051 | \n", "7 | \n", "19080 | \n", "13807 | \n", "24353 | \n", "34 | \n", "25 | \n", "43 | \n", "FR | \n", "France | \n", "
1581 | \n", "1581 | \n", "199050 | \n", "7 | \n", "11079 | \n", "6660 | \n", "15498 | \n", "20 | \n", "12 | \n", "28 | \n", "FR | \n", "France | \n", "
1582 | \n", "1582 | \n", "199049 | \n", "7 | \n", "1143 | \n", "0 | \n", "2610 | \n", "2 | \n", "0 | \n", "5 | \n", "FR | \n", "France | \n", "
1583 rows × 11 columns
\n", "