diff --git a/module3/exo2/exercice.ipynb b/module3/exo2/exercice.ipynb index 0bbbe371b01e359e381e43239412d77bf53fb1fb..0b7e0249a81680636efb3691121e635153e9c64b 100644 --- a/module3/exo2/exercice.ipynb +++ b/module3/exo2/exercice.ipynb @@ -1,5 +1,1357 @@ { - "cells": [], + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Exercice 03 - 2 " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Récupération des données de l'incidence de la varicelle " + ] + }, + { + "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\n", + "import os.path\n", + "\n", + "data_url = \"http://www.sentiweb.fr/datasets/incidence-PAY-7.csv\"" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "(Exo 1) 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`.\n", + "\n", + "Nous copions ensuite les données dans un fichier local. Si le fichier local n'existe pas, les données sont téléchargé depuis le site internet. Cela nous permet de garder un jeux de donnée dans le cas où le site serait ammené à ne plus fonctionner. " + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "data_file = \"syndrome-varicelle.csv\"\n", + "\n", + "import os\n", + "import urllib.request\n", + "if not os.path.exists(data_file):\n", + " urllib.request.urlretrieve(data_url, data_file)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Nous récupérons ainsi les données." + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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weekindicatorincinc_lowinc_upinc100inc100_lowinc100_upgeo_inseegeo_name
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.................................
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1548 rows × 10 columns

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weekindicatorincinc_lowinc_upinc100inc100_lowinc100_upgeo_inseegeo_name
\n", + "
" + ], + "text/plain": [ + "Empty DataFrame\n", + "Columns: [week, indicator, inc, inc_low, inc_up, inc100, inc100_low, inc100_up, geo_insee, geo_name]\n", + "Index: []" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "raw_data[raw_data.isnull().any(axis=1)]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Non, nous n'avons donc de nettoyage à faire. " + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "(Exo 1) Nos données utilisent une convention inhabituelle: le numéro de semaine est collé à l'année, donnant l'impression qu'il s'agit 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 semaine. Il faut lui fournir les dates de début et de fin de semaine. Nous utilisons pour cela la bibliothèque isoweek.\n", + "\n", + "Comme la conversion des semaines est devenu assez complexe, nous écrivons une petite fonction Python pour cela. Ensuite, nous l'appliquons à tous les points de nos donnés. Les résultats vont dans une nouvelle colonne 'period'." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "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": [ + "(Exo 1) 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": 7, + "metadata": {}, + "outputs": [], + "source": [ + "sorted_data = data.set_index('period').sort_index()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "(Exo 1) 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." + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "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": [ + "(Exo 1) Nous définissons la période de référence\n", + "entre deux minima de l'incidence, du 1er septembre de l'année $N$ au\n", + "1er septembre 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 septembre de chaque année, nous utilisons le\n", + "premier jour de la semaine qui contient le 1er septembre.\n", + "\n", + "Encore un petit détail: les données commencent an octobre 1990, ce qui\n", + "rend la première année incomplète. Nous commençons donc l'analyse en 1991." + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "first_september_week = [pd.Period(pd.Timestamp(y, 9, 1), 'W')\n", + " for y in range(1991,\n", + " sorted_data.index[-1].year)]" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "(Exo 1) En partant de cette liste des semaines qui contiennent un 1er septembre, 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": 15, + "metadata": {}, + "outputs": [], + "source": [ + "year = []\n", + "yearly_incidence = []\n", + "for week1, week2 in zip(first_september_week[:-1],\n", + " first_september_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": [ + "(Exo 1) Voici les incidences annuelles." + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + }, + { + "data": { + "image/png": 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\n", 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" + ] + }, + "metadata": { + "needs_background": "light" + }, + "output_type": "display_data" + } + ], + "source": [ + "yearly_incidence.plot(style='*')" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Maintenant que nous avons la liste d'incidence par année. Nous pouvons dans un premier temps récupérer l'année avec le plus fort taux d'incidence pour l'exercice 2" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "## Taux d'incidence par année" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "2002 516689\n", + "2018 542312\n", + "2017 551041\n", + "1996 564901\n", + "2019 584066\n", + "2015 604382\n", + "2000 617597\n", + "2001 619041\n", + "2012 624573\n", + "2005 628464\n", + "2006 632833\n", + "2011 642368\n", + "1993 643387\n", + "1995 652478\n", + "1994 661409\n", + "1998 677775\n", + "1997 683434\n", + "2014 685769\n", + "2013 698332\n", + "2007 717352\n", + "2008 749478\n", + "1999 756456\n", + "2003 758363\n", + "2004 777388\n", + "2016 782114\n", + "2010 829911\n", + "1992 832939\n", + "2009 842373\n", + "dtype: int64" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "yearly_incidence.sort_values()" + ] + } + ], "metadata": { "kernelspec": { "display_name": "Python 3", @@ -16,10 +1368,9 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.6.3" + "version": "3.6.4" } }, "nbformat": 4, "nbformat_minor": 2 } -