{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Incidence of chickenpox-like illness in France"
   ]
  },
  {
   "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": [
    "The data on the incidence of chickenpox-like illness are available from the Web site of the [Réseau Sentinelles](http://www.sentiweb.fr/). We download them as a file in CSV format, in which each line corresponds to a week in the observation period. Only the complete dataset, starting in 1991 and ending with a recent week, is available for download."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "data_url = \"http://www.sentiweb.fr/datasets/incidence-PAY-7.csv\""
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This is the documentation of the data from [the download site](https://ns.sentiweb.fr/incidence/csv-schema-v1.json):\n",
    "\n",
    "| Column name  | Description                                                                                                               |\n",
    "|--------------|---------------------------------------------------------------------------------------------------------------------------|\n",
    "| `week`       | ISO8601 Yearweek number as numeric (year times 100 + week nubmer)                                                               |\n",
    "| `indicator`  | Unique identifier of the indicator, see metadata document https://www.sentiweb.fr/meta.json                               |\n",
    "| `inc`        | Estimated incidence value for the time step, in the geographic level                                                      |\n",
    "| `inc_low`    | Lower bound of the estimated incidence 95% Confidence Interval                                                            |\n",
    "| `inc_up`     | Upper bound of the estimated incidence 95% Confidence Interval                                                            |\n",
    "| `inc100`     | Estimated rate incidence per 100,000 inhabitants                                                                          |\n",
    "| `inc100_low` | Lower bound of the estimated incidence 95% Confidence Interval                                                            |\n",
    "| `inc100_up`  | Upper bound of the estimated rate incidence 95% Confidence Interval                                                       |\n",
    "| `geo_insee`  | Identifier of the geographic area, from INSEE https://www.insee.fr                                                        |\n",
    "| `geo_name`   | Geographic label of the area, corresponding to INSEE code. This label is not an id and is only provided for human reading |\n",
    "\n",
    "The first line of the CSV file is a comment, which we ignore with `skip=1`."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Check that the local file does not exist before downloading"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import urllib.request\n",
    "\n",
    "data_file = \"incidence-PAY-7.csv\"\n",
    "\n",
    "if not os.path.exists(data_file):\n",
    "    urllib.request.urlretrieve(data_url, data_file)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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