diff --git a/.gitattributes b/.gitattributes
index 82abb1befbd3ddd66cbd86aec552b019b866ebf2..4f061036e19362921c3c2f3701cf1d79b20711ea 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -239,3 +239,4 @@ data/covid-19-italy/dati-province-description.json filter=lfs diff=lfs merge=lfs
data/covid-19-italy/dati-regioni-description.json filter=lfs diff=lfs merge=lfs -text
data/covid-19-italy/dati-andamento-nazionale-description.json filter=lfs diff=lfs merge=lfs -text
data/openzh-covid-19/COVID19_Fallzahlen_Kanton_SO_total.csv filter=lfs diff=lfs merge=lfs -text
+figures/* !text !filter !merge !diff
diff --git a/notebooks/examples/openzh-covid-19-example.ipynb b/notebooks/examples/openzh-covid-19-example.ipynb
index c8e62282c388a1372d7dcb39d2d8c5ff13f2336b..04aaea51692ddaafad9bb597c89399ac66a0a622 100644
--- a/notebooks/examples/openzh-covid-19-example.ipynb
+++ b/notebooks/examples/openzh-covid-19-example.ipynb
@@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 1,
+ "execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
@@ -13,23 +13,56 @@
"from IPython.display import display, HTML"
]
},
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "tags": [
+ "parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "save_figures = False\n",
+ "data_path = '../../data/openzh-covid-19'\n",
+ "figures_path = '../../figures'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 104,
+ "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"
+ "## 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": 2,
+ "execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"# read in cantonal data and produce one dataframe\n",
"df_list = []\n",
"\n",
- "for f in Path('../../data/openzh-covid-19/').glob('COVID19_Fallzahlen_Kanton_*total.csv'):\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",
@@ -39,7 +72,37 @@
},
{
"cell_type": "code",
- "execution_count": 3,
+ "execution_count": 103,
+ "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}_10k'] = df.apply(\n",
+ " lambda row: row[f'ncumul_{x}']/pop_d['Total'][row.abbreviation_canton_and_fl]*10000, axis=1\n",
+ " )"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 99,
"metadata": {},
"outputs": [
{
@@ -74,8 +137,12 @@
" <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>TotalPosTests1</th>\n",
" <th>TotalCured</th>\n",
+ " <th>ncumul_conf_per10k</th>\n",
+ " <th>ncumul_conf_10k</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
@@ -94,6 +161,10 @@
" <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>0.029074</td>\n",
+ " <td>0.029074</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
@@ -110,6 +181,10 @@
" <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>0.058147</td>\n",
+ " <td>0.058147</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
@@ -126,6 +201,10 @@
" <td>https://www.vs.ch/de/web/coronavirus/info?p_p_...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0.087221</td>\n",
+ " <td>0.087221</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
@@ -142,6 +221,10 @@
" <td>https://www.vs.ch/de/web/coronavirus/info?p_p_...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0.145368</td>\n",
+ " <td>0.145368</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
@@ -158,6 +241,10 @@
" <td>https://www.vs.ch/de/web/coronavirus/info?p_p_...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0.203515</td>\n",
+ " <td>0.203515</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -178,22 +265,29 @@
"3 NaN NaN NaN NaN NaN \n",
"4 NaN NaN NaN NaN NaN \n",
"\n",
- " source TotalPosTests1 \\\n",
- "0 https://vs.ch/documents/529400/6767345/2020+02... NaN \n",
- "1 https://vs.ch/documents/529400/6789273/2020+03... NaN \n",
- "2 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n",
- "3 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n",
- "4 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n",
+ " source ncumul_ICF \\\n",
+ "0 https://vs.ch/documents/529400/6767345/2020+02... NaN \n",
+ "1 https://vs.ch/documents/529400/6789273/2020+03... NaN \n",
+ "2 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n",
+ "3 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n",
+ "4 https://www.vs.ch/de/web/coronavirus/info?p_p_... NaN \n",
"\n",
- " TotalCured \n",
- "0 NaN \n",
- "1 NaN \n",
- "2 NaN \n",
- "3 NaN \n",
- "4 NaN "
+ " ncumul_ICU_intub TotalPosTests1 TotalCured ncumul_conf_per10k \\\n",
+ "0 NaN NaN NaN 0.029074 \n",
+ "1 NaN NaN NaN 0.058147 \n",
+ "2 NaN NaN NaN 0.087221 \n",
+ "3 NaN NaN NaN 0.145368 \n",
+ "4 NaN NaN NaN 0.203515 \n",
+ "\n",
+ " ncumul_conf_10k \n",
+ "0 0.029074 \n",
+ "1 0.058147 \n",
+ "2 0.087221 \n",
+ "3 0.145368 \n",
+ "4 0.203515 "
]
},
- "execution_count": 3,
+ "execution_count": 99,
"metadata": {},
"output_type": "execute_result"
}
@@ -207,22 +301,55 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "## Plot the available data"
+ "## Plot the available data\n",
+ "\n",
+ "Below we make plots of total cases, total cases per 10k population and total deaths. "
]
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": 105,
+ "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('ncumul_conf',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": 105,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
- "<div id=\"altair-viz-e5add070879b4309a07c932dcb6e845a\"></div>\n",
+ "<div id=\"altair-viz-6d584701c7bf4b3c8ef6c5b808e39bf1\"></div>\n",
"<script type=\"text/javascript\">\n",
" (function(spec, embedOpt){\n",
- " const outputDiv = document.getElementById(\"altair-viz-e5add070879b4309a07c932dcb6e845a\");\n",
+ " const outputDiv = document.getElementById(\"altair-viz-6d584701c7bf4b3c8ef6c5b808e39bf1\");\n",
" const paths = {\n",
" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
" \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
@@ -263,11 +390,11 @@
" .catch(showError)\n",
" .then(() => displayChart(vegaEmbed));\n",
" }\n",
- " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"data\": {\"name\": \"data-c2a3c4f5fdbd4123fccf4a11f31204b6\"}, \"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"legend\": {\"title\": \"Canton\"}}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"title\": \"Cumulative\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"scale\": {\"type\": \"log\"}, \"title\": \"Cases\"}}, \"title\": \"Covid-19 cases in Switzerland by Canton\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-c2a3c4f5fdbd4123fccf4a11f31204b6\": [{\"date\": \"2020-02-28T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 1.0, \"ncumul_hosp\": null, \"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\", \"TotalPosTests1\": null, \"TotalCured\": null}, {\"date\": \"2020-03-03T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 2.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://vs.ch/documents/529400/6789273/2020+03+03+-+Medienmitteilung+-+Best%C3%A4tigung+2.+Fall.pdf/9e063e45-70a1-682e-fc37-31d9685f71f1?t=1583233390225\", \"TotalPosTests1\": null, \"TotalCured\": null}, {\"date\": \"2020-03-05T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 3.0, \"ncumul_hosp\": 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\"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=4#collapse6846567\", \"TotalPosTests1\": null, \"TotalCured\": null}, {\"date\": \"2020-03-10T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 18.0, \"ncumul_hosp\": 4.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": 3.0, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=3#collapse6858802\", \"TotalPosTests1\": null, \"TotalCured\": null}, {\"date\": \"2020-03-11T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 22.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": null, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=3#collapse6870561\", \"TotalPosTests1\": null, \"TotalCured\": null}, {\"date\": \"2020-03-13T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 22.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=3#collapse6898881\", \"TotalPosTests1\": null, \"TotalCured\": null}, {\"date\": \"2020-03-17T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 95.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 3.0, \"source\": 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null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 6.813254877671105, \"ncumul_conf_10k\": 6.813254877671105}]}}, {\"mode\": \"vega-lite\"});\n",
"</script>"
],
"text/plain": [
- "alt.Chart(...)"
+ "alt.HConcatChart(...)"
]
},
"metadata": {},
@@ -277,8 +404,11 @@
"data": {
"text/html": [
"\n",
- "<p style=\"font-size: smaller\">Data Source: \n",
- " <a href=\"https://github.com/openZH/covid_19.git\">OpenData Zuerich</a>,\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>"
],
@@ -291,25 +421,144 @@
}
],
"source": [
- "chart = alt.Chart(\n",
- " df.where(df.ncumul_conf>0).dropna(subset=['abbreviation_canton_and_fl']), title='Covid-19 cases in Switzerland by Canton'\n",
- ").mark_line().encode(\n",
- " alt.X('date', title='Date'), \n",
- " alt.Y('ncumul_conf', \n",
- " title='Cases', scale=alt.Scale(type='log')),\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('ncumul_conf',title='Cumulative')]\n",
+ "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",
- "chart.configure_header(titleFontSize=25)\n",
- "chart.configure_axis(labelFontSize=15, titleFontSize=15)\n",
+ "\n",
"display(chart)\n",
- "display(HTML('''\n",
- "<p style=\"font-size: smaller\">Data Source: \n",
- " <a href=\"https://github.com/openZH/covid_19.git\">OpenData Zuerich</a>,\n",
- " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
- "</p>'''))"
+ "if save_figures:\n",
+ " chart.save(str(Path(figures_path) / 'switzerland-cases-by-canton.png'), webdriver='firefox')\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": 117,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-019ec480415444409e707caa5776407f\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-019ec480415444409e707caa5776407f\");\n",
+ " 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\": \"selector023\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"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\": {\"selector023\": {\"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\": \"selector024\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"abbreviation_canton_and_fl\", \"title\": \"Canton\"}, {\"type\": \"quantitative\", \"field\": \"ncumul_conf\", \"title\": \"Deaths/10k\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"ncumul_deceased_10k\", \"scale\": {\"type\": \"linear\"}, \"title\": \"Deaths per 10k population\"}}, \"selection\": {\"selector024\": {\"type\": \"multi\", \"fields\": [\"abbreviation_canton_and_fl\"], \"bind\": \"legend\"}}}], \"data\": {\"name\": \"data-b8d19ec6f5366f902a1a5e8b2c091f24\"}, \"title\": \"Covid-19 deaths in Switzerland by Canton\", \"$schema\": 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\"ncumul_deceased_10k\": 0.02907357067058191}, {\"date\": \"2020-03-17T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 95.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 3.0, \"source\": \"https://www.vs.ch/de/web/coronavirus/info?p_p_id=com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN&p_p_lifecycle=0&p_p_state=normal&p_p_mode=view&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_delta=5&p_r_p_resetCur=false&_com_liferay_asset_publisher_web_portlet_AssetPublisherPortlet_INSTANCE_1rjMHS5sCcaN_cur=2#collapse6927494\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 2.7619892137052813, \"ncumul_conf_10k\": 2.7619892137052813, \"ncumul_deceased_10k\": 0.08722071201174572}, {\"date\": \"2020-03-19T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 232.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 4.0, \"source\": \"https://www.vs.ch/de/web/coronavirus#collapse6955818\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 6.745068395575003, \"ncumul_conf_10k\": 6.745068395575003, \"ncumul_deceased_10k\": 0.11629428268232764}, {\"date\": \"2020-03-20T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 282.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 5.0, \"source\": \"https://www.vs.ch/de/web/coronavirus\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 8.198746929104098, \"ncumul_conf_10k\": 8.198746929104098, \"ncumul_deceased_10k\": 0.14536785335290953}, {\"date\": \"2020-03-21T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 359.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 9.0, \"source\": \"https://www.vs.ch/de/web/coronavirus\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 10.437411870738904, \"ncumul_conf_10k\": 10.437411870738904, \"ncumul_deceased_10k\": 0.2616621360352372}, {\"date\": \"2020-03-22T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VS\", \"ncumul_tested\": null, \"ncumul_conf\": 432.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 10.0, \"source\": \"https://www.vs.ch/de/web/coronavirus\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 12.559782529691383, \"ncumul_conf_10k\": 12.559782529691383, \"ncumul_deceased_10k\": 0.29073570670581905}, {\"date\": \"2020-03-18T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"GR\", \"ncumul_tested\": null, \"ncumul_conf\": 116.0, \"ncumul_hosp\": 13.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.gr.ch/DE/institutionen/verwaltung/djsg/ga/coronavirus/info/Seiten/Start.aspx\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 5.847393121247713, \"ncumul_conf_10k\": 5.847393121247713, \"ncumul_deceased_10k\": 0.05040856139006649}, {\"date\": \"2020-03-19T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"GR\", \"ncumul_tested\": null, \"ncumul_conf\": 145.0, \"ncumul_hosp\": 18.0, \"ncumul_ICU\": null, \"ncumul_vent\": null, 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null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 12.955000277247088, \"ncumul_conf_10k\": 12.955000277247088, \"ncumul_deceased_10k\": 0.25204280695033243}, {\"date\": \"2020-03-16T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"BE\", \"ncumul_tested\": null, \"ncumul_conf\": 123.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.besondere-lage.sites.be.ch/besondere-lage_sites/de/index/corona/index.html\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 1.1884322067060429, \"ncumul_conf_10k\": 1.1884322067060429, \"ncumul_deceased_10k\": 0.009662050461024736}, {\"date\": \"2020-03-18T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"BE\", \"ncumul_tested\": null, \"ncumul_conf\": 193.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.besondere-lage.sites.be.ch/besondere-lage_sites/de/index/corona/index.html\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 1.8647757389777744, \"ncumul_conf_10k\": 1.8647757389777744, \"ncumul_deceased_10k\": 0.009662050461024736}, {\"date\": \"2020-03-19T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"BE\", \"ncumul_tested\": null, \"ncumul_conf\": 282.0, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.besondere-lage.sites.be.ch/besondere-lage_sites/de/index/corona/index.html\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 2.724698230008976, \"ncumul_conf_10k\": 2.724698230008976, \"ncumul_deceased_10k\": 0.009662050461024736}, {\"date\": 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0.01251337366810779}, {\"date\": \"2020-03-12T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 156.0, \"ncumul_hosp\": 43.0, \"ncumul_ICU\": 8.0, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 1.9520862922248154, \"ncumul_conf_10k\": 1.9520862922248154, \"ncumul_deceased_10k\": 0.01251337366810779}, {\"date\": \"2020-03-13T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 204.0, \"ncumul_hosp\": 52.0, \"ncumul_ICU\": 10.0, \"ncumul_vent\": null, \"ncumul_released\": 5.0, \"ncumul_deceased\": 2.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 2.552728228293989, \"ncumul_conf_10k\": 2.552728228293989, \"ncumul_deceased_10k\": 0.02502674733621558}, {\"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, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 4.379680783837727, \"ncumul_conf_10k\": 4.379680783837727, \"ncumul_deceased_10k\": 0.03754012100432337}, {\"date\": \"2020-03-15T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 406.0, \"ncumul_hosp\": 62.0, \"ncumul_ICU\": 19.0, \"ncumul_vent\": null, \"ncumul_released\": 5.0, \"ncumul_deceased\": 4.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 5.080429709251763, \"ncumul_conf_10k\": 5.080429709251763, \"ncumul_deceased_10k\": 0.05005349467243116}, {\"date\": \"2020-03-16T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 508.0, \"ncumul_hosp\": 66.0, \"ncumul_ICU\": 27.0, \"ncumul_vent\": null, \"ncumul_released\": 5.0, \"ncumul_deceased\": 5.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 6.356793823398758, \"ncumul_conf_10k\": 6.356793823398758, \"ncumul_deceased_10k\": 0.06256686834053896}, {\"date\": \"2020-03-17T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 608.0, \"ncumul_hosp\": 95.0, \"ncumul_ICU\": 35.0, \"ncumul_vent\": null, \"ncumul_released\": 9.0, \"ncumul_deceased\": 5.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 7.608131190209536, \"ncumul_conf_10k\": 7.608131190209536, \"ncumul_deceased_10k\": 0.06256686834053896}, {\"date\": \"2020-03-18T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 796.0, \"ncumul_hosp\": 128.0, \"ncumul_ICU\": 34.0, \"ncumul_vent\": null, \"ncumul_released\": 16.0, \"ncumul_deceased\": 5.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 9.960645439813803, \"ncumul_conf_10k\": 9.960645439813803, \"ncumul_deceased_10k\": 0.06256686834053896}, {\"date\": \"2020-03-19T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 1212.0, \"ncumul_hosp\": 140.0, \"ncumul_ICU\": 32.0, \"ncumul_vent\": null, \"ncumul_released\": 52.0, \"ncumul_deceased\": 7.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 15.166208885746641, \"ncumul_conf_10k\": 15.166208885746641, \"ncumul_deceased_10k\": 0.08759361567675453}, {\"date\": \"2020-03-20T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 1432.0, \"ncumul_hosp\": 152.0, \"ncumul_ICU\": 30.0, \"ncumul_vent\": null, \"ncumul_released\": 62.0, \"ncumul_deceased\": 12.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 17.919151092730356, \"ncumul_conf_10k\": 17.919151092730356, \"ncumul_deceased_10k\": 0.15016048401729348}, {\"date\": \"2020-03-21T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"VD\", \"ncumul_tested\": null, \"ncumul_conf\": 1676.0, \"ncumul_hosp\": 175.0, \"ncumul_ICU\": 23.0, \"ncumul_vent\": null, \"ncumul_released\": 70.0, \"ncumul_deceased\": 15.0, \"source\": \"https://www.vd.ch/toutes-les-actualites/hotline-et-informations-sur-le-coronavirus/\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": 20.972414267748654, \"ncumul_conf_10k\": 20.972414267748654, \"ncumul_deceased_10k\": 0.18770060502161687}, {\"date\": \"2020-03-21T00:00:00\", \"time\": null, \"abbreviation_canton_and_fl\": \"AR\", \"ncumul_tested\": null, \"ncumul_conf\": null, \"ncumul_hosp\": null, \"ncumul_ICU\": null, \"ncumul_vent\": null, \"ncumul_released\": null, \"ncumul_deceased\": 1.0, \"source\": \"https://www.ar.ch/schnellzugriff/medienmitteilungen-der-kantonalen-verwaltung/detail/news/coronavirus-erster-todesfall-in-appenzell-ausserrhoden/?tx_news_pi1%5Bcontroller%5D=News&tx_news_pi1%5Baction%5D=detail&cHash=a88f209df29c38474f9c5f9e1c5dd53f\", \"ncumul_ICF\": null, \"ncumul_ICU_intub\": null, \"TotalPosTests1\": null, \"TotalCured\": null, \"ncumul_conf_per10k\": null, \"ncumul_conf_10k\": null, \"ncumul_deceased_10k\": 0.6193868070610096}]}}, {\"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.png'), webdriver='firefox')\n",
+ " chart.save(str(Path(figures_path) / 'switzerland-deaths-by-canton.html'))\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
}
],
"metadata": {
diff --git a/requirements.txt b/requirements.txt
index 2bc49958b6cd110a8a5284d2e4f6826a7e404c13..3640d140f9e3eb7f0480d5e10f5925043e7ae143 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -106,4 +106,5 @@ vega-datasets==0.8.0
wcwidth==0.1.8
webencodings==0.5.1
yarl==1.4.2
+xlrd
zipp==3.0.0