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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\n",
"from IPython.display import display, HTML"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"tags": [
"parameters"
]
},
"outputs": [],
"source": [
"save_figures = False\n",
"data_path = '../../data/openzh-covid-19'\n",
"figures_path = '../../figures'"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"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>''')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Read in the data\n",
"\n",
"We have two datasets for Switzerland - the COVID-19 dataset from https://github.com/openZH/covid_19 and the population statistics by age and canton. We can read both of these in to dataframes:"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"# 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)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"# 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}_100k'] = df.apply(\n",
" lambda row: row[f'ncumul_{x}']/pop_d['Total'][row.abbreviation_canton_and_fl]*100000, axis=1\n",
" )"
]
},
{
"cell_type": "code",
"execution_count": 6,
"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>time</th>\n",
" <th>abbreviation_canton_and_fl</th>\n",
" <th>ncumul_tested</th>\n",
" <th>ncumul_conf</th>\n",
" <th>ncumul_hosp</th>\n",
" <th>ncumul_ICU</th>\n",
" <th>ncumul_vent</th>\n",
" <th>ncumul_released</th>\n",
" <th>ncumul_deceased</th>\n",
" <th>source</th>\n",
" <th>ncumul_ICF</th>\n",
" <th>ncumul_ICU_intub</th>\n",
" <th>ncumul_deceased_suspect</th>\n",
" <th>TotalPosTests1</th>\n",
" <th>TotalCured</th>\n",
" <th>ncumul_conf_100k</th>\n",
" <th>ncumul_deceased_100k</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>2020-02-28</td>\n",
" <td>NaN</td>\n",
" <td>VS</td>\n",
" <td>NaN</td>\n",
" <td>1.0</td>\n",
" <td>3.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>https://vs.ch/documents/529400/6767345/2020+02...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.290736</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2020-02-29</td>\n",
" <td>NaN</td>\n",
" <td>VS</td>\n",
" <td>NaN</td>\n",
" <td>1.0</td>\n",
" <td>3.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>https://www.vs.ch/documents/6756452/7008787/Si...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.290736</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2020-03-01</td>\n",
" <td>NaN</td>\n",
" <td>VS</td>\n",
" <td>NaN</td>\n",
" <td>2.0</td>\n",
" <td>4.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>https://www.vs.ch/documents/6756452/7008787/Si...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.581471</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>2020-03-02</td>\n",
" <td>NaN</td>\n",
" <td>VS</td>\n",
" <td>NaN</td>\n",
" <td>3.0</td>\n",
" <td>4.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>https://www.vs.ch/documents/6756452/7008787/Si...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.872207</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>2020-03-03</td>\n",
" <td>NaN</td>\n",
" <td>VS</td>\n",
" <td>NaN</td>\n",
" <td>3.0</td>\n",
" <td>5.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>https://vs.ch/documents/529400/6789273/2020+03...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>0.872207</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" date time abbreviation_canton_and_fl ncumul_tested ncumul_conf \\\n",
"0 2020-02-28 NaN VS NaN 1.0 \n",
"1 2020-02-29 NaN VS NaN 1.0 \n",
"2 2020-03-01 NaN VS NaN 2.0 \n",
"3 2020-03-02 NaN VS NaN 3.0 \n",
"4 2020-03-03 NaN VS NaN 3.0 \n",
"\n",
" ncumul_hosp ncumul_ICU ncumul_vent ncumul_released ncumul_deceased \\\n",
"0 3.0 NaN NaN NaN NaN \n",
"1 3.0 NaN NaN NaN NaN \n",
"2 4.0 NaN NaN NaN NaN \n",
"3 4.0 NaN NaN NaN NaN \n",
"4 5.0 NaN NaN NaN NaN \n",
"\n",
" source ncumul_ICF \\\n",
"0 https://vs.ch/documents/529400/6767345/2020+02... NaN \n",
"1 https://www.vs.ch/documents/6756452/7008787/Si... NaN \n",
"2 https://www.vs.ch/documents/6756452/7008787/Si... NaN \n",
"3 https://www.vs.ch/documents/6756452/7008787/Si... NaN \n",
"4 https://vs.ch/documents/529400/6789273/2020+03... NaN \n",
"\n",
" ncumul_ICU_intub ncumul_deceased_suspect TotalPosTests1 TotalCured \\\n",
"0 NaN NaN NaN NaN \n",
"1 NaN NaN NaN NaN \n",
"2 NaN NaN NaN NaN \n",
"3 NaN NaN NaN NaN \n",
"4 NaN NaN NaN NaN \n",
"\n",
" ncumul_conf_100k ncumul_deceased_100k \n",
"0 0.290736 NaN \n",
"1 0.290736 NaN \n",
"2 0.581471 NaN \n",
"3 0.872207 NaN \n",
"4 0.872207 NaN "
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]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# display the dataframe\n",
"df.head()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Plot the available data\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. "
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"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"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Total cases"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"<div id=\"altair-viz-77300a88a4ac46bbb5ba0a2d3d51684c\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
" const outputDiv = document.getElementById(\"altair-viz-77300a88a4ac46bbb5ba0a2d3d51684c\");\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",
" \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
" \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
" };\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",
" s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
" document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
" });\n",
" }\n",
"\n",
" function showError(err) {\n",
" outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
" throw err;\n",
" }\n",
"\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",
" displayChart(vegaEmbed);\n",
" } else {\n",
" loadScript(\"vega\")\n",
" .then(() => loadScript(\"vega-lite\"))\n",
" .then(() => loadScript(\"vega-embed\"))\n",
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
" })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector005\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"title\": \"Cases\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Cases\"}}, \"selection\": {\"selector005\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}, {\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector006\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf_100k\", \"title\": \"Cases/100k\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf_100k\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Cases per 100k population\"}}, \"selection\": {\"selector006\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}], \"data\": {\"name\": \"data-2efedca1243d5f65c801c94b7ae4c3ea\"}, \"title\": \"Covid-19 cases in Switzerland by Canton\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-2efedca1243d5f65c801c94b7ae4c3ea\": [{\"date\": \"2020-02-28T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 1.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://vs.ch/documents/529400/6767345/2020+02+28+-+Medienmitteilung+-+1.+Fall+Coronavirus+VS.pdf/37c4f942-c5d5-6ab5-64fd-83444de4eba5?t=1582923242156\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.2907357067058191, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-02-29T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 1.0, \"ncumul_hosp\": 3.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.2907357067058191, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-01T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 2.0, \"ncumul_hosp\": 4.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 0.5814714134116382, \"ncumul_deceased_100k\": null}, {\"date\": \"2020-03-02T00:00:00\", \"time\": null, 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],
"text/plain": [
"alt.HConcatChart(...)"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"ename": "ImportError",
"evalue": "selenium package is required for saving chart as svg",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mModuleNotFoundError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/altair/utils/headless.py\u001b[0m in \u001b[0;36mcompile_spec\u001b[0;34m(spec, format, mode, vega_version, vegaembed_version, vegalite_version, scale_factor, driver_timeout, webdriver)\u001b[0m\n\u001b[1;32m 114\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 115\u001b[0;31m \u001b[0;32mimport\u001b[0m \u001b[0mselenium\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mwebdriver\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 116\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mImportError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'selenium'",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mImportError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-10-06ee86bb9189>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[0mchart\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msave\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mPath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfigures_path\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m/\u001b[0m \u001b[0;34m'switzerland-cases-by-canton.html'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 17\u001b[0;31m \u001b[0mchart\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msave\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mPath\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfigures_path\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m/\u001b[0m \u001b[0;34m'switzerland-cases-by-canton.svg'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 18\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 19\u001b[0m \u001b[0mdisplay\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhtml_credits\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/altair/vegalite/v4/api.py\u001b[0m in \u001b[0;36msave\u001b[0;34m(self, fp, format, override_data_transformer, scale_factor, vegalite_version, vega_version, vegaembed_version, **kwargs)\u001b[0m\n\u001b[1;32m 445\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0moverride_data_transformer\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 446\u001b[0m \u001b[0;32mwith\u001b[0m \u001b[0mdata_transformers\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdisable_max_rows\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 447\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msave\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 448\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 449\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0msave\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0mkwds\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/altair/utils/save.py\u001b[0m in \u001b[0;36msave\u001b[0;34m(chart, fp, vega_version, vegaembed_version, format, mode, vegalite_version, embed_options, json_kwds, webdriver, scale_factor, **kwargs)\u001b[0m\n\u001b[1;32m 100\u001b[0m \u001b[0mvegaembed_version\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mvegaembed_version\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 101\u001b[0m \u001b[0mwebdriver\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mwebdriver\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 102\u001b[0;31m scale_factor=scale_factor, **kwargs)\n\u001b[0m\u001b[1;32m 103\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mformat\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'png'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 104\u001b[0m \u001b[0mwrite_file_or_filename\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mfp\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmimebundle\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'image/png'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmode\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;34m'wb'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/altair/utils/mimebundle.py\u001b[0m in \u001b[0;36mspec_to_mimebundle\u001b[0;34m(spec, format, mode, vega_version, vegaembed_version, vegalite_version, **kwargs)\u001b[0m\n\u001b[1;32m 54\u001b[0m \u001b[0mvega_version\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mvega_version\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 55\u001b[0m \u001b[0mvegaembed_version\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mvegaembed_version\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 56\u001b[0;31m vegalite_version=vegalite_version, **kwargs)\n\u001b[0m\u001b[1;32m 57\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mformat\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m'png'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 58\u001b[0m \u001b[0mrender\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mbase64\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mb64decode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrender\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m','\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mencode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m/opt/conda/lib/python3.7/site-packages/altair/utils/headless.py\u001b[0m in \u001b[0;36mcompile_spec\u001b[0;34m(spec, format, mode, vega_version, vegaembed_version, vegalite_version, scale_factor, driver_timeout, webdriver)\u001b[0m\n\u001b[1;32m 116\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mImportError\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 117\u001b[0m raise ImportError(\"selenium package is required \"\n\u001b[0;32m--> 118\u001b[0;31m \"for saving chart as {}\".format(format))\n\u001b[0m\u001b[1;32m 119\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 120\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mformat\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32min\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0;34m'png'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'svg'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'vega'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mImportError\u001b[0m: selenium package is required for saving chart as svg"
]
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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_100k = generate_canton_chart('ncumul_conf_100k', 'Cases per 100k population', 'Cases/100k')\n",
"\n",
"chart = alt.hconcat(\n",
" cumul, cumul_100k, 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)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Deaths"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
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" \"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",
" function loadScript(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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" })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector003\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_deceased\", \"title\": \"Deaths\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_deceased\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Deaths\"}}, \"selection\": {\"selector003\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}, {\"mark\": \"line\", 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\"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 28.49209925717027, \"ncumul_deceased_100k\": 0.2907357067058191}, {\"date\": \"2020-03-16T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 116.0, \"ncumul_hosp\": 24.0, \"ncumul_ICU\": 1.0, \"ncumul_vent\": 1.0, \"ncumul_released\": null, \"ncumul_deceased\": 2.0, \"source\": \"https://www.vs.ch/documents/6756452/7008787/Sit%20Epid%20-%20%C3%89tat%20Stand%2025.03.2020.pdf\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 33.72534197787501, \"ncumul_deceased_100k\": 0.5814714134116382}, {\"date\": \"2020-03-17T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": 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\"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 25.527282282939893, \"ncumul_deceased_100k\": 0.2502674733621558}, {\"date\": \"2020-03-14T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 350.0, \"ncumul_hosp\": 43.0, \"ncumul_ICU\": 14.0, \"ncumul_vent\": null, \"ncumul_released\": 5.0, \"ncumul_deceased\": 3.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"ncumul_deceased_suspect\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_100k\": 43.79680783837727, \"ncumul_deceased_100k\": 0.3754012100432337}, {\"date\": \"2020-03-15T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", 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"</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_100k = generate_canton_chart('ncumul_deceased_100k', 'Deaths per 100k population', 'Deaths/100k')\n",
"\n",
"chart = alt.hconcat(\n",
" deaths, deaths_100k, 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"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"hide_input": true,
"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": "3.7.3"
}
},
"nbformat": 4,
"nbformat_minor": 4
}