{
"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",
"for f in Path('../../data/openzh-covid-19/').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": 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",
" <td>2020-02-28</td>\n",
" <td>Canton_BL</td>\n",
" <td>NaN</td>\n",
" <td>1</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>https://www.baselland.ch/politik-und-behorden/...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>2020-02-29</td>\n",
" <td>Canton_BL</td>\n",
" <td>NaN</td>\n",
" <td>2</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>https://www.baselland.ch/politik-und-behorden/...</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>2020-03-01</td>\n",
" <td>Canton_BL</td>\n",
" <td>NaN</td>\n",
" <td>2</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",
" <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",
" <th>11</th>\n",
" <td>2020-03-12</td>\n",
" <td>Canton_ZH</td>\n",
" <td>NaN</td>\n",
" <td>92</td>\n",
" <td>NaN</td>\n",
" <td>7.0</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>12</th>\n",
" <td>2020-03-13</td>\n",
" <td>Canton_ZH</td>\n",
" <td>NaN</td>\n",
" <td>140</td>\n",
" <td>NaN</td>\n",
" <td>11.0</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>13</th>\n",
" <td>2020-03-16</td>\n",
" <td>Canton_ZH</td>\n",
" <td>NaN</td>\n",
" <td>270</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>14</th>\n",
" <td>2020-03-17</td>\n",
" <td>Canton_ZH</td>\n",
" <td>NaN</td>\n",
" <td>294</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",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>2020-03-18</td>\n",
" <td>Canton_ZH</td>\n",
" <td>NaN</td>\n",
" <td>424</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",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>75 rows × 12 columns</p>\n",
"</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",
"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",
".. ... ... ... ... ... \n",
"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",
"\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",
"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",
"\n",
" Source Source2 Source3 \\\n",
"0 NaN NaN NaN \n",
"1 NaN NaN NaN \n",
"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",
".. ... ... ... \n",
"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",
"\n",
" Unnamed: 11 \n",
"0 NaN \n",
"1 NaN \n",
"0 NaN \n",
"1 NaN \n",
"2 NaN \n",
".. ... \n",
"11 NaN \n",
"12 NaN \n",
"13 NaN \n",
"14 NaN \n",
"15 NaN \n",
"\n",
"[75 rows x 12 columns]"
]
},
"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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" const outputDiv = document.getElementById(\"altair-viz-0dc4f9b9fee5403e9ce1b7e9c219a9f0\");\n",
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" \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
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" vegaEmbed(outputDiv, spec, embedOpt)\n",
" .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
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"\n",
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" })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"data\": {\"name\": \"data-a1f62021ac6cee94dbfc4af2257f04ca\"}, \"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"Area\"}, \"x\": {\"type\": \"temporal\", \"field\": \"Date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"TotalConfCases\"}}, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-a1f62021ac6cee94dbfc4af2257f04ca\": [{\"Date\": \"2020-03-16T00:00:00\", \"Area\": \"Canton_BE\", \"TotalTestedCases\": null, \"TotalConfCases\": 123, \"TotalPosTests1\": 131.0, \"TotalCured\": null, \"TotalDeaths\": 1.0, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-18T00:00:00\", \"Area\": \"Canton_BE\", \"TotalTestedCases\": null, \"TotalConfCases\": 193, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 1.0, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-02-28T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 1, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/neuer-coronavirus-covid-19-erster-bestaetigter-fall-aus-dem-kanton-basel-landschaft\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-02-29T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 2, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/weiterer-bestaetigter-fall-aus-dem-kanton-basel-landschaft\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-01T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 2, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-02T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 2, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-03T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 2, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-04T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 2, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-05T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 6, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/neuer-coronavirus-covid-19-sechs-bestaetigte-faelle-im-kanton-basel-landschaft\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-06T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 6, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-07T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 15, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": null, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/update-15-bestaetigte-faelle-in-basel-landschaft\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-08T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 19, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 1.0, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/patient-im-kantonsspital-baselland-stirbt-an-den-folgen-einer-coronavirus-infektion\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-09T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 20, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 1.0, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/update-xx-bestaetigte-faelle-in-basel-landschaft\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-10T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 22, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 1.0, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/update\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-11T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 26, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 2.0, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/update-26-bestaetigte-faelle-in-basel-landschaft-1\", \"Source2\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/zweiter-baselbieter-patient-stirbt-an-den-folgen-einer-covid-19-infektion\", \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-12T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 26, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 2.0, \"TotalHospitalized\": null, \"Source\": null, \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-13T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 42, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 2.0, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/update-26-bestaetigte-faelle-in-basel-landschaft-2\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-14T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 47, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 2.0, \"TotalHospitalized\": null, \"Source\": \"https://www.baselland.ch/politik-und-behorden/direktionen/volkswirtschafts-und-gesundheitsdirektion/medienmitteilungen/update-47-bestaetigte-faelle-in-basel-landschaft\", \"Source2\": null, \"Source3\": null, \"Unnamed: 11\": null}, {\"Date\": \"2020-03-15T00:00:00\", \"Area\": \"Canton_BL\", \"TotalTestedCases\": null, \"TotalConfCases\": 54, \"TotalPosTests1\": null, \"TotalCured\": null, \"TotalDeaths\": 2.0, \"TotalHospitalized\": null, \"Source\": 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