openzh-covid-19-dashboard.ipynb

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   "source": [
    "from pathlib import Path\n",
    "\n",
    "import altair as alt\n",
    "import pandas as pd\n",
    "from IPython.display import display, HTML"
   ]
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     "parameters"
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   "source": [
    "save_figures = False\n",
    "data_path = '../data/openzh-covid-19'"
   ]
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    "html_credits=HTML('''\n",
    "<p style=\"font-size: smaller\">Data Sources: \n",
    "  <a href=\"https://github.com/openZH/covid_19\">OpenData Zuerich</a>,\n",
    "  <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
    "<br>\n",
    "Analysis:\n",
    "  <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
    "</p>''')"
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    "## Summary data for Covid-19 cases in Switzerland\n",
    "\n",
    "The data for Switzerland comes from the effort initiated by [OpenData Zürich](https://github.com/openZH/covid_19) and collected during the [Case data #covid19mon hackathon challenge](https://db.schoolofdata.ch/project/73). \n",
    "\n",
    "Below we make plots of total cases, total cases per 10k population and total deaths. You can click on the canton abbreviations in the legend to highlight individual lines. "
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    "# read in cantonal data and produce one dataframe\n",
    "df_list = []\n",
    "\n",
    "for f in Path(data_path).glob('COVID19_Fallzahlen_Kanton_*total.csv'):\n",
    "    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)"
   ]
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    "# read in population data\n",
    "df_pop = pd.read_excel(\n",
    "    Path(data_path) / '../ch-population-statistics/ch-population-by-age-canton.xls', \n",
    "    header=1, \n",
    "    skipfooter=5\n",
    ")\n",
    "df_pop = df_pop.where(\n",
    "    df_pop.Region.str.startswith('-')\n",
    ").dropna().sort_values('Region').reset_index(drop=True)\n",
    "\n",
    "# match the cantons in the two datasets\n",
    "df_pop['abbreviation_canton_and_fl'] = ['AG', 'AI', 'AR', 'BL', 'BS', 'BE', 'FR', 'GE', 'GL', 'GR', 'JU', 'LU', 'NE', 'NW', 'OW', 'SH', 'SZ', 'SO', 'SG', 'TG', 'TI', 'UR', 'VS', 'VD', 'ZG', 'ZH']\n",
    "\n",
    "pop_d = df_pop[['abbreviation_canton_and_fl', 'Total']].set_index('abbreviation_canton_and_fl').to_dict()\n",
    "\n",
    "\n",
    "# calculate cases and deaths per 10k\n",
    "\n",
    "for x in ['conf', 'deceased']:\n",
    "    df[f'ncumul_{x}_10k'] = df.apply(\n",
    "        lambda row: row[f'ncumul_{x}']/pop_d['Total'][row.abbreviation_canton_and_fl]*10000, axis=1\n",
    "    )"
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    "def generate_canton_chart(column, title, tooltip_title):\n",
    "    \"\"\"Produce a canton chart given a column name\"\"\"\n",
    "    selection = alt.selection_multi(fields=['abbreviation_canton_and_fl'], bind='legend')\n",
    "    chart = base.mark_line().encode(\n",
    "        alt.X('date', title='Date'), \n",
    "        alt.Y(column, \n",
    "              title=title, scale=alt.Scale(type='linear')),\n",
    "        color=alt.Color('abbreviation_canton_and_fl', legend=alt.Legend(title=\"Canton\")),\n",
    "        tooltip=[alt.Tooltip('abbreviation_canton_and_fl',title='Canton'),\n",
    "                 alt.Tooltip(column,title=tooltip_title),\n",
    "                 alt.Tooltip('date',title='Date')],\n",
    "        opacity=alt.condition(selection, alt.value(1), alt.value(0.2))\n",
    "    ).add_selection(\n",
    "        selection\n",
    "    )\n",
    "    return chart"
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   "cell_type": "markdown",
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   "source": [
    "### Total cases"
   ]
  },
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   "cell_type": "code",
   "execution_count": 11,
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\"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 10.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.suedostschweiz.ch/ereignisse/2020-03-20/die-zahl-der-corona-faelle-im-glarnerland-steigt-stark-an\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 2.4750637328911216, \"ncumul_deceased_10k\": null}, {\"date\": \"2020-03-19T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"GL\", \"ncumul_tested\": null, \"ncumul_conf\": 17.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.suedostschweiz.ch/ereignisse/2020-03-20/die-zahl-der-corona-faelle-im-glarnerland-steigt-stark-an\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, 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null, \"source\": \"https://sh.ch/CMS/Webseite/Kanton-Schaffhausen/Beh-rde/Verwaltung/Departement-des-Innern/Gesundheitsamt-3209198-DE.html\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 1.7075044821992655, \"ncumul_deceased_10k\": null}, {\"date\": \"2020-03-23T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"SH\", \"ncumul_tested\": null, \"ncumul_conf\": 30.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://sh.ch/CMS/Webseite/Kanton-Schaffhausen/Beh-rde/Verwaltung/Departement-des-Innern/Gesundheitsamt-3209198-DE.html\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 3.658938176141284, \"ncumul_deceased_10k\": null}, {\"date\": \"2020-03-24T00:00:00\", \"time\": 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       "</script>"
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      "text/plain": [
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     "metadata": {},
     "output_type": "display_data"
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       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/openZH/covid_19\">OpenData Zuerich</a>,\n",
       "  <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
       "<br>\n",
       "Analysis:\n",
       "  <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
       "</p>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
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   "source": [
    "base = alt.Chart(df.where(df.ncumul_conf>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
    "base.configure_header(titleFontSize=25)\n",
    "base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
    "\n",
    "cumul = generate_canton_chart('ncumul_conf', 'Cases', 'Cases')\n",
    "cumul_10k = generate_canton_chart('ncumul_conf_10k', 'Cases per 10k population', 'Cases/10k')\n",
    "\n",
    "chart = alt.hconcat(\n",
    "    cumul, cumul_10k, title='Covid-19 cases in Switzerland by Canton'\n",
    ").configure_title(\n",
    "    anchor='middle'\n",
    ")\n",
    "\n",
    "display(chart)\n",
    "if save_figures:\n",
    "    chart.save(str(Path(figures_path) / 'switzerland-cases-by-canton.html'))\n",
    "    \n",
    "display(html_credits)"
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  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Deaths"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "jupyter": {
     "source_hidden": true
    }
   },
   "outputs": [
    {
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\"https://www.ar.ch/verwaltung/departement-gesundheit-und-soziales/amt-fuer-gesundheit/informationsseite-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 18.58160421183029, \"ncumul_deceased_10k\": 0.6193868070610096}, {\"date\": \"2020-03-24T00:00:00\", \"time\": \"10:00\", \"abbreviation_canton_and_fl\": \"AR\", \"ncumul_tested\": null, \"ncumul_conf\": 33.0, \"ncumul_hosp\": 6.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 2.0, \"source\": \"https://www.ar.ch/verwaltung/departement-gesundheit-und-soziales/amt-fuer-gesundheit/informationsseite-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_10k\": 20.439764633013315, \"ncumul_deceased_10k\": 1.2387736141220191}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.HConcatChart(...)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/openZH/covid_19\">OpenData Zuerich</a>,\n",
       "  <a href=\"https://www.bfs.admin.ch\">Federal Statistical Office</a>\n",
       "<br>\n",
       "Analysis:\n",
       "  <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
       "</p>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "base = alt.Chart(df.where(df.ncumul_deceased>0).dropna(subset=['abbreviation_canton_and_fl']))\n",
    "base.configure_header(titleFontSize=25)\n",
    "base.configure_axis(labelFontSize=15, titleFontSize=15)\n",
    "\n",
    "deaths = generate_canton_chart('ncumul_deceased', 'Deaths', 'Deaths')\n",
    "deaths_10k = generate_canton_chart('ncumul_deceased_10k', 'Deaths per 10k population', 'Deaths/10k')\n",
    "\n",
    "chart = alt.hconcat(\n",
    "    deaths, deaths_10k, title='Covid-19 deaths in Switzerland by Canton'\n",
    ").configure_title(\n",
    "    anchor='middle'\n",
    ")\n",
    "display(chart)    \n",
    "display(html_credits)\n",
    "\n",
    "if save_figures:\n",
    "    chart.save(str(Path(figures_path) / 'switzerland-deaths-by-canton.html'))\n"
   ]
  }
 ],
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