{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Incidence du syndrome grippal" ] }, { "cell_type": "code", "execution_count": null, "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": null, "metadata": { "collapsed": true }, "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": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
weekindicatorincinc_lowinc_upinc100inc100_lowinc100_upgeo_inseegeo_name
020251732753720985.034089.04131.051.0FRFrance
120251632886422770.034958.04334.052.0FRFrance
220251533572129592.041850.05344.062.0FRFrance
320251433757931232.043926.05647.065.0FRFrance
420251333967333686.045660.05950.068.0FRFrance
520251235254345627.059459.07868.088.0FRFrance
620251135946952154.066784.08978.0100.0FRFrance
720251036033453048.067620.09079.0101.0FRFrance
820250938453174994.094068.0126112.0140.0FRFrance
92025083136020124824.0147216.0203186.0220.0FRFrance
102025073208952195988.0221916.0312293.0331.0FRFrance
112025063273519258159.0288879.0408385.0431.0FRFrance
122025053334395318416.0350374.0499475.0523.0FRFrance
132025043350043332885.0367201.0522496.0548.0FRFrance
142025033252772238917.0266627.0377356.0398.0FRFrance
152025023257247242991.0271503.0384363.0405.0FRFrance
162025013231549214627.0248471.0345320.0370.0FRFrance
172024523201726185870.0217582.0302278.0326.0FRFrance
182024513201697187843.0215551.0302281.0323.0FRFrance
192024503136694126369.0147019.0205190.0220.0FRFrance
20202449310848799037.0117937.0163149.0177.0FRFrance
2120244838738178687.096075.0131118.0144.0FRFrance
2220244737628667626.084946.0114101.0127.0FRFrance
2320244635639949006.063792.08574.096.0FRFrance
2420244534734740843.053851.07161.081.0FRFrance
2520244433603930122.041956.05445.063.0FRFrance
2620244334657239928.053216.07060.080.0FRFrance
2720244236778560009.075561.010290.0114.0FRFrance
2820244137943571386.087484.0119107.0131.0FRFrance
2920244038496576555.093375.0127114.0140.0FRFrance
.................................
208319852132609619621.032571.04735.059.0FRFrance
208419852032789620885.034907.05138.064.0FRFrance
208519851934315432821.053487.07859.097.0FRFrance
208619851834055529935.051175.07455.093.0FRFrance
208719851733405324366.043740.06244.080.0FRFrance
208819851635036236451.064273.09166.0116.0FRFrance
208919851536388145538.082224.011683.0149.0FRFrance
20901985143134545114400.0154690.0244207.0281.0FRFrance
20911985133197206176080.0218332.0357319.0395.0FRFrance
20921985123245240223304.0267176.0445405.0485.0FRFrance
20931985113276205252399.0300011.0501458.0544.0FRFrance
20941985103353231326279.0380183.0640591.0689.0FRFrance
20951985093369895341109.0398681.0670618.0722.0FRFrance
20961985083389886359529.0420243.0707652.0762.0FRFrance
20971985073471852432599.0511105.0855784.0926.0FRFrance
20981985063565825518011.0613639.01026939.01113.0FRFrance
20991985053637302592795.0681809.011551074.01236.0FRFrance
21001985043424937390794.0459080.0770708.0832.0FRFrance
21011985033213901174689.0253113.0388317.0459.0FRFrance
210219850239758680949.0114223.0177147.0207.0FRFrance
210319850138548965918.0105060.0155120.0190.0FRFrance
210419845238483060602.0109058.0154110.0198.0FRFrance
2105198451310172680242.0123210.0185146.0224.0FRFrance
21061984503123680101401.0145959.0225184.0266.0FRFrance
2107198449310107381684.0120462.0184149.0219.0FRFrance
210819844837862060634.096606.0143110.0176.0FRFrance
210919844737202954274.089784.013199.0163.0FRFrance
211019844638733067686.0106974.0159123.0195.0FRFrance
21111984453135223101414.0169032.0246184.0308.0FRFrance
211219844436842220056.0116788.012537.0213.0FRFrance
\n", "

2113 rows × 10 columns

\n", "
" ], "text/plain": [ " week indicator inc inc_low inc_up inc100 inc100_low \\\n", "0 202517 3 27537 20985.0 34089.0 41 31.0 \n", "1 202516 3 28864 22770.0 34958.0 43 34.0 \n", "2 202515 3 35721 29592.0 41850.0 53 44.0 \n", "3 202514 3 37579 31232.0 43926.0 56 47.0 \n", "4 202513 3 39673 33686.0 45660.0 59 50.0 \n", "5 202512 3 52543 45627.0 59459.0 78 68.0 \n", "6 202511 3 59469 52154.0 66784.0 89 78.0 \n", "7 202510 3 60334 53048.0 67620.0 90 79.0 \n", "8 202509 3 84531 74994.0 94068.0 126 112.0 \n", "9 202508 3 136020 124824.0 147216.0 203 186.0 \n", "10 202507 3 208952 195988.0 221916.0 312 293.0 \n", "11 202506 3 273519 258159.0 288879.0 408 385.0 \n", "12 202505 3 334395 318416.0 350374.0 499 475.0 \n", "13 202504 3 350043 332885.0 367201.0 522 496.0 \n", "14 202503 3 252772 238917.0 266627.0 377 356.0 \n", "15 202502 3 257247 242991.0 271503.0 384 363.0 \n", "16 202501 3 231549 214627.0 248471.0 345 320.0 \n", "17 202452 3 201726 185870.0 217582.0 302 278.0 \n", "18 202451 3 201697 187843.0 215551.0 302 281.0 \n", "19 202450 3 136694 126369.0 147019.0 205 190.0 \n", "20 202449 3 108487 99037.0 117937.0 163 149.0 \n", "21 202448 3 87381 78687.0 96075.0 131 118.0 \n", "22 202447 3 76286 67626.0 84946.0 114 101.0 \n", "23 202446 3 56399 49006.0 63792.0 85 74.0 \n", "24 202445 3 47347 40843.0 53851.0 71 61.0 \n", "25 202444 3 36039 30122.0 41956.0 54 45.0 \n", "26 202443 3 46572 39928.0 53216.0 70 60.0 \n", "27 202442 3 67785 60009.0 75561.0 102 90.0 \n", "28 202441 3 79435 71386.0 87484.0 119 107.0 \n", "29 202440 3 84965 76555.0 93375.0 127 114.0 \n", "... ... ... ... ... ... ... ... \n", "2083 198521 3 26096 19621.0 32571.0 47 35.0 \n", "2084 198520 3 27896 20885.0 34907.0 51 38.0 \n", "2085 198519 3 43154 32821.0 53487.0 78 59.0 \n", "2086 198518 3 40555 29935.0 51175.0 74 55.0 \n", "2087 198517 3 34053 24366.0 43740.0 62 44.0 \n", "2088 198516 3 50362 36451.0 64273.0 91 66.0 \n", "2089 198515 3 63881 45538.0 82224.0 116 83.0 \n", "2090 198514 3 134545 114400.0 154690.0 244 207.0 \n", "2091 198513 3 197206 176080.0 218332.0 357 319.0 \n", "2092 198512 3 245240 223304.0 267176.0 445 405.0 \n", "2093 198511 3 276205 252399.0 300011.0 501 458.0 \n", "2094 198510 3 353231 326279.0 380183.0 640 591.0 \n", "2095 198509 3 369895 341109.0 398681.0 670 618.0 \n", "2096 198508 3 389886 359529.0 420243.0 707 652.0 \n", "2097 198507 3 471852 432599.0 511105.0 855 784.0 \n", "2098 198506 3 565825 518011.0 613639.0 1026 939.0 \n", "2099 198505 3 637302 592795.0 681809.0 1155 1074.0 \n", "2100 198504 3 424937 390794.0 459080.0 770 708.0 \n", "2101 198503 3 213901 174689.0 253113.0 388 317.0 \n", "2102 198502 3 97586 80949.0 114223.0 177 147.0 \n", "2103 198501 3 85489 65918.0 105060.0 155 120.0 \n", "2104 198452 3 84830 60602.0 109058.0 154 110.0 \n", "2105 198451 3 101726 80242.0 123210.0 185 146.0 \n", "2106 198450 3 123680 101401.0 145959.0 225 184.0 \n", "2107 198449 3 101073 81684.0 120462.0 184 149.0 \n", "2108 198448 3 78620 60634.0 96606.0 143 110.0 \n", "2109 198447 3 72029 54274.0 89784.0 131 99.0 \n", "2110 198446 3 87330 67686.0 106974.0 159 123.0 \n", "2111 198445 3 135223 101414.0 169032.0 246 184.0 \n", "2112 198444 3 68422 20056.0 116788.0 125 37.0 \n", "\n", " inc100_up geo_insee geo_name \n", "0 51.0 FR France \n", "1 52.0 FR France \n", "2 62.0 FR France \n", "3 65.0 FR France \n", "4 68.0 FR France \n", "5 88.0 FR France \n", "6 100.0 FR France \n", "7 101.0 FR France \n", "8 140.0 FR France \n", "9 220.0 FR France \n", "10 331.0 FR France \n", "11 431.0 FR France \n", "12 523.0 FR France \n", "13 548.0 FR France \n", "14 398.0 FR France \n", "15 405.0 FR France \n", "16 370.0 FR France \n", "17 326.0 FR France \n", "18 323.0 FR France \n", "19 220.0 FR France \n", "20 177.0 FR France \n", "21 144.0 FR France \n", "22 127.0 FR France \n", "23 96.0 FR France \n", "24 81.0 FR France \n", "25 63.0 FR France \n", "26 80.0 FR France \n", "27 114.0 FR France \n", "28 131.0 FR France \n", "29 140.0 FR France \n", "... ... ... ... \n", "2083 59.0 FR France \n", "2084 64.0 FR France \n", "2085 97.0 FR France \n", "2086 93.0 FR France \n", "2087 80.0 FR France \n", "2088 116.0 FR France \n", "2089 149.0 FR France \n", "2090 281.0 FR France \n", "2091 395.0 FR France \n", "2092 485.0 FR France \n", "2093 544.0 FR France \n", "2094 689.0 FR France \n", "2095 722.0 FR France \n", "2096 762.0 FR France \n", "2097 926.0 FR France \n", "2098 1113.0 FR France \n", "2099 1236.0 FR France \n", "2100 832.0 FR France \n", "2101 459.0 FR France \n", "2102 207.0 FR France \n", "2103 190.0 FR France \n", "2104 198.0 FR France \n", "2105 224.0 FR France \n", "2106 266.0 FR France \n", "2107 219.0 FR France \n", "2108 176.0 FR France \n", "2109 163.0 FR France \n", "2110 195.0 FR France \n", "2111 308.0 FR France \n", "2112 213.0 FR France \n", "\n", "[2113 rows x 10 columns]" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "raw_data = pd.read_csv('inc-3-PAY.csv', 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": null, "metadata": {}, "outputs": [], "source": [ "raw_data[raw_data.isnull().any(axis=1)]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Nous éliminons ce point, ce qui n'a pas d'impact fort sur notre analyse qui est assez simple." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "data = raw_data.dropna().copy()\n", "data" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Nos données utilisent une convention inhabituelle: le numéro de\n", "semaine est collé à l'année, donnant l'impression qu'il s'agit\n", "de nombre entier. C'est comme ça que Pandas les interprète.\n", " \n", "Un deuxième problème est que Pandas ne comprend pas les numéros de\n", "semaine. Il faut lui fournir les dates de début et de fin de\n", "semaine. Nous utilisons pour cela la bibliothèque `isoweek`.\n", "\n", "Comme la conversion des semaines est devenu assez complexe, nous\n", "écrivons une petite fonction Python pour cela. Ensuite, nous\n", "l'appliquons à tous les points de nos donnés. Les résultats vont\n", "dans une nouvelle colonne 'period'." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "def convert_week(year_and_week_int):\n", " year_and_week_str = str(year_and_week_int)\n", " year = int(year_and_week_str[:4])\n", " week = int(year_and_week_str[4:])\n", " w = isoweek.Week(year, week)\n", " return pd.Period(w.day(0), 'W')\n", "\n", "data['period'] = [convert_week(yw) for yw in data['week']]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Il restent deux petites modifications à faire.\n", "\n", "Premièrement, nous définissons les périodes d'observation\n", "comme nouvel index de notre jeux de données. Ceci en fait\n", "une suite chronologique, ce qui sera pratique par la suite.\n", "\n", "Deuxièmement, nous trions les points par période, dans\n", "le sens chronologique." ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "sorted_data = data.set_index('period').sort_index()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Nous vérifions la cohérence des données. Entre la fin d'une période et\n", "le début de la période qui suit, la différence temporelle doit être\n", "zéro, ou au moins très faible. Nous laissons une \"marge d'erreur\"\n", "d'une seconde.\n", "\n", "Ceci s'avère tout à fait juste sauf pour deux périodes consécutives\n", "entre lesquelles il manque une semaine.\n", "\n", "Nous reconnaissons ces dates: c'est la semaine sans observations\n", "que nous avions supprimées !" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "periods = sorted_data.index\n", "for p1, p2 in zip(periods[:-1], periods[1:]):\n", " delta = p2.to_timestamp() - p1.end_time\n", " if delta > pd.Timedelta('1s'):\n", " print(p1, p2)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Un premier regard sur les données !" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "sorted_data['inc'].plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Un zoom sur les dernières années montre mieux la situation des pics en hiver. Le creux des incidences se trouve en été." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "sorted_data['inc'][-200:].plot()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Etude de l'incidence annuelle" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Etant donné que le pic de l'épidémie se situe en hiver, à cheval\n", "entre deux années civiles, nous définissons la période de référence\n", "entre deux minima de l'incidence, du 1er août de l'année $N$ au\n", "1er août de l'année $N+1$.\n", "\n", "Notre tâche est un peu compliquée par le fait que l'année ne comporte\n", "pas un nombre entier de semaines. Nous modifions donc un peu nos périodes\n", "de référence: à la place du 1er août de chaque année, nous utilisons le\n", "premier jour de la semaine qui contient le 1er août.\n", "\n", "Comme l'incidence de syndrome grippal est très faible en été, cette\n", "modification ne risque pas de fausser nos conclusions.\n", "\n", "Encore un petit détail: les données commencent an octobre 1984, ce qui\n", "rend la première année incomplète. Nous commençons donc l'analyse en 1985." ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [ "first_august_week = [pd.Period(pd.Timestamp(y, 8, 1), 'W')\n", " for y in range(1985,\n", " sorted_data.index[-1].year)]" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "En partant de cette liste des semaines qui contiennent un 1er août, nous obtenons nos intervalles d'environ un an comme les périodes entre deux semaines adjacentes dans cette liste. Nous calculons les sommes des incidences hebdomadaires pour toutes ces périodes.\n", "\n", "Nous vérifions également que ces périodes contiennent entre 51 et 52 semaines, pour nous protéger contre des éventuelles erreurs dans notre code." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "year = []\n", "yearly_incidence = []\n", "for week1, week2 in zip(first_august_week[:-1],\n", " first_august_week[1:]):\n", " one_year = sorted_data['inc'][week1:week2-1]\n", " assert abs(len(one_year)-52) < 2\n", " yearly_incidence.append(one_year.sum())\n", " year.append(week2.year)\n", "yearly_incidence = pd.Series(data=yearly_incidence, index=year)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Voici les incidences annuelles." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "yearly_incidence.plot(style='*')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Une liste triée permet de plus facilement répérer les valeurs les plus élevées (à la fin)." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "yearly_incidence.sort_values()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Enfin, un histogramme montre bien que les épidémies fortes, qui touchent environ 10% de la population\n", " française, sont assez rares: il y en eu trois au cours des 35 dernières années." ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "yearly_incidence.hist(xrot=20)" ] }, { "cell_type": "code", "execution_count": null, "metadata": { "collapsed": true }, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.4" } }, "nbformat": 4, "nbformat_minor": 1 }