chickenpox

module3/exo2/chickenpox-like-illness-analysis.ipynb

+{
+ "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": []
+  }
+ ],
+ "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": 2
+}

module3/exo2/exercice.ipynb

-{
- "cells": [],
- "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": "3.6.3"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}
-