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openzh-covid-19-example.ipynb 40.1 KiB
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{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from pathlib import Path\n",
    "\n",
    "import altair as alt\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Read in the data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# read in cantonal data and produce one dataframe\n",
    "df_list = []\n",
    "\n",
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    "for f in Path('../../data/openzh-covid-19/').glob('COVID19_Fallzahlen_Kanton_*total.csv'):\n",
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    "    df_list.append(pd.read_csv(f))\n",
    "\n",
    "df = pd.concat(df_list)\n",
    "\n",
    "df['Date'] = pd.to_datetime(df['Date'], dayfirst=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Date</th>\n",
       "      <th>Area</th>\n",
       "      <th>TotalTestedCases</th>\n",
       "      <th>TotalConfCases</th>\n",
       "      <th>TotalPosTests1</th>\n",
       "      <th>TotalCured</th>\n",
       "      <th>TotalDeaths</th>\n",
       "      <th>TotalHospitalized</th>\n",
       "      <th>Source</th>\n",
       "      <th>Source2</th>\n",
       "      <th>Source3</th>\n",
       "      <th>Unnamed: 11</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2020-03-16</td>\n",
       "      <td>Canton_BE</td>\n",
       "      <td>NaN</td>\n",
       "      <td>123</td>\n",
       "      <td>131.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2020-03-18</td>\n",
       "      <td>Canton_BE</td>\n",
       "      <td>NaN</td>\n",
       "      <td>193</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
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       "      <td>2020-02-28</td>\n",
       "      <td>Canton_BL</td>\n",
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       "      <td>NaN</td>\n",
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       "      <td>1</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>https://www.baselland.ch/politik-und-behorden/...</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
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       "      <td>2020-02-29</td>\n",
       "      <td>Canton_BL</td>\n",
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       "      <td>NaN</td>\n",
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       "      <td>2</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>https://www.baselland.ch/politik-und-behorden/...</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
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       "      <td>2020-03-01</td>\n",
       "      <td>Canton_BL</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "      <th>11</th>\n",
       "      <td>2020-03-12</td>\n",
       "      <td>Canton_ZH</td>\n",
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       "      <td>NaN</td>\n",
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       "      <td>92</td>\n",
       "      <td>NaN</td>\n",
       "      <td>7.0</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "      <th>12</th>\n",
       "      <td>2020-03-13</td>\n",
       "      <td>Canton_ZH</td>\n",
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       "      <td>NaN</td>\n",
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       "      <td>140</td>\n",
       "      <td>NaN</td>\n",
       "      <td>11.0</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "      <th>13</th>\n",
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       "      <td>2020-03-16</td>\n",
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       "      <td>Canton_ZH</td>\n",
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       "      <td>NaN</td>\n",
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       "      <td>270</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "      <th>14</th>\n",
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       "      <td>2020-03-17</td>\n",
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       "      <td>Canton_ZH</td>\n",
       "      <td>NaN</td>\n",
       "      <td>294</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
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       "      <th>15</th>\n",
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       "      <td>2020-03-18</td>\n",
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       "      <td>Canton_ZH</td>\n",
       "      <td>NaN</td>\n",
       "      <td>424</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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       "<p>75 rows × 12 columns</p>\n",
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       "</div>"
      ],
      "text/plain": [
       "         Date       Area  TotalTestedCases  TotalConfCases  TotalPosTests1  \\\n",
       "0  2020-03-16  Canton_BE               NaN             123           131.0   \n",
       "1  2020-03-18  Canton_BE               NaN             193             NaN   \n",
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       "0  2020-02-28  Canton_BL               NaN               1             NaN   \n",
       "1  2020-02-29  Canton_BL               NaN               2             NaN   \n",
       "2  2020-03-01  Canton_BL               NaN               2             NaN   \n",
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       "..        ...        ...               ...             ...             ...   \n",
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       "11 2020-03-12  Canton_ZH               NaN              92             NaN   \n",
       "12 2020-03-13  Canton_ZH               NaN             140             NaN   \n",
       "13 2020-03-16  Canton_ZH               NaN             270             NaN   \n",
       "14 2020-03-17  Canton_ZH               NaN             294             NaN   \n",
       "15 2020-03-18  Canton_ZH               NaN             424             NaN   \n",
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       "\n",
       "    TotalCured  TotalDeaths  TotalHospitalized  \\\n",
       "0          NaN          1.0                NaN   \n",
       "1          NaN          1.0                NaN   \n",
       "0          NaN          NaN                NaN   \n",
       "1          NaN          NaN                NaN   \n",
       "2          NaN          NaN                NaN   \n",
       "..         ...          ...                ...   \n",
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       "11         7.0          NaN                NaN   \n",
       "12        11.0          NaN                NaN   \n",
       "13         NaN          1.0                NaN   \n",
       "14         NaN          NaN                NaN   \n",
       "15         NaN          NaN                NaN   \n",
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       "\n",
       "                                               Source Source2 Source3  \\\n",
       "0                                                 NaN     NaN     NaN   \n",
       "1                                                 NaN     NaN     NaN   \n",
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       "0   https://www.baselland.ch/politik-und-behorden/...     NaN     NaN   \n",
       "1   https://www.baselland.ch/politik-und-behorden/...     NaN     NaN   \n",
       "2                                                 NaN     NaN     NaN   \n",
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       "..                                                ...     ...     ...   \n",
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       "11                                                NaN     NaN     NaN   \n",
       "12                                                NaN     NaN     NaN   \n",
       "13                                                NaN     NaN     NaN   \n",
       "14                                                NaN     NaN     NaN   \n",
       "15                                                NaN     NaN     NaN   \n",
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       "\n",
       "    Unnamed: 11  \n",
       "0           NaN  \n",
       "1           NaN  \n",
       "0           NaN  \n",
       "1           NaN  \n",
       "2           NaN  \n",
       "..          ...  \n",
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       "11          NaN  \n",
       "12          NaN  \n",
       "13          NaN  \n",
       "14          NaN  \n",
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       "15          NaN  \n",
       "\n",
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       "[75 rows x 12 columns]"
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      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# display the dataframe\n",
    "df"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Plot the available data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
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       "<div id=\"altair-viz-0dc4f9b9fee5403e9ce1b7e9c219a9f0\"></div>\n",
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       "<script type=\"text/javascript\">\n",
       "  (function(spec, embedOpt){\n",
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       "    const outputDiv = document.getElementById(\"altair-viz-0dc4f9b9fee5403e9ce1b7e9c219a9f0\");\n",
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       "    const paths = {\n",
       "      \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
       "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
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       "    };\n",
       "\n",
       "    function loadScript(lib) {\n",
       "      return new Promise(function(resolve, reject) {\n",
       "        var s = document.createElement('script');\n",
       "        s.src = paths[lib];\n",
       "        s.async = true;\n",
       "        s.onload = () => resolve(paths[lib]);\n",
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       "\n",
       "    function displayChart(vegaEmbed) {\n",
       "      vegaEmbed(outputDiv, spec, embedOpt)\n",
       "        .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
       "    }\n",
       "\n",
       "    if(typeof define === \"function\" && define.amd) {\n",
       "      requirejs.config({paths});\n",
       "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
       "    } else if (typeof vegaEmbed === \"function\") {\n",
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       "      loadScript(\"vega\")\n",
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       "        .then(() => loadScript(\"vega-embed\"))\n",
       "        .catch(showError)\n",
       "        .then(() => displayChart(vegaEmbed));\n",
       "    }\n",
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376 
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\"TotalTestedCases\": null, \"TotalConfCases\": 2, \"TotalPosTests1\": 2.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-02T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 2, \"TotalPosTests1\": 9.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-03T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": 400.0, \"TotalConfCases\": 9, \"TotalPosTests1\": 13.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-05T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 19, \"TotalPosTests1\": 19.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-06T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 26, \"TotalPosTests1\": 26.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-07T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 30, \"TotalPosTests1\": 30.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-08T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 37, \"TotalPosTests1\": 37.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-09T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": 855.0, \"TotalConfCases\": 40, \"TotalPosTests1\": 40.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-10T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 49, \"TotalPosTests1\": 49.0, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-11T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 59, \"TotalPosTests1\": 59.0, \"TotalCured\": 1.0, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-12T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 92, \"TotalPosTests1\": null, \"TotalCured\": 7.0, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-13T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 140, \"TotalPosTests1\": null, \"TotalCured\": 11.0, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-16T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 270, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 1.0, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-17T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 294, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-18T00:00:00\", \"Area\": \"Canton_ZH\", \"TotalTestedCases\": null, \"TotalConfCases\": 424, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}]}}, {\"mode\": \"vega-lite\"});\n",
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add example notebook for open data ch
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       "</script>"
      ],
      "text/plain": [
       "alt.Chart(...)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "alt.Chart(df).mark_line().encode(x='Date', y='TotalConfCases', color='Area')"
   ]
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zh open data notebook update  
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  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
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  }
 ],
 "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",
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fix: corrected path to new location of notebook  
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   "version": "3.7.6"
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  }
 },
 "nbformat": 4,
 "nbformat_minor": 4
}

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