From 24fcb29a8610d9141a075a770a7eb118730cfeae Mon Sep 17 00:00:00 2001
From: Paul Ronga <paul.ronga@laposte.net>
Date: Sun, 9 Aug 2020 18:08:06 +0000
Subject: [PATCH] Notebook for cases and deaths in Swiss cantons
---
covid-19-swiss-cantons.ipynb | 900 +++++++++++++++++++++++++++++++++++
1 file changed, 900 insertions(+)
create mode 100644 covid-19-swiss-cantons.ipynb
diff --git a/covid-19-swiss-cantons.ipynb b/covid-19-swiss-cantons.ipynb
new file mode 100644
index 00000000..d7f8fdea
--- /dev/null
+++ b/covid-19-swiss-cantons.ipynb
@@ -0,0 +1,900 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import warnings\n",
+ "from IPython.display import display, HTML\n",
+ "import altair as alt"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "html_credits=HTML('''\n",
+ "<p style=\"font-size: smaller\">Data Source: \n",
+ " <a href=\"https://www.bag.admin.ch/bag/en/home/krankheiten/ausbrueche-epidemien-pandemien/aktuelle-ausbrueche-epidemien/novel-cov/situation-schweiz-und-international.html\">Federal Office of Public Health FOPH</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">Covid-19 Public Data Collaboration Project</a>\n",
+ "</p>''')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Load BAG data: “Fallzahlen zu den Laborbefunden und Todesfällen (XLS, 7 MB, 09.08.2020)â€\n",
+ "# Very slow download\n",
+ "df = pd.read_excel('https://www.bag.admin.ch/dam/bag/fr/dokumente/mt/k-und-i/aktuelle-ausbrueche-pandemien/2019-nCoV/covid-19-basisdaten-fallzahlen.xlsx.download.xlsx/Dashboards_1&2_COVID19_swiss_data_pv.xlsx')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "assert df.columns.tolist() == ['replikation_dt', 'fall_dt', 'ktn', 'akl', 'sex', 'Geschlecht', 'Sexe',\n",
+ " 'fallklasse_3', 'pttoddat', 'pttod_1'], 'Error: column names changed'"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def translateGender(value):\n",
+ " if value == 'homme':\n",
+ " return 'male'\n",
+ " elif value == 'femme':\n",
+ " return 'female'\n",
+ " elif value == 'manquant':\n",
+ " return 'unknown'\n",
+ " else:\n",
+ " warnings.warn(\"Unknown value:\", value)\n",
+ " return ''\n",
+ "\n",
+ "df['gender'] = df['Sexe'].apply(translateGender)\n",
+ "del df['Sexe']\n",
+ "del df['Geschlecht']"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "df['akl'] = df['akl'].apply(lambda x: x.replace('Unbekannt', 'unknown'))"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "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>replikation_dt</th>\n",
+ " <th>fall_dt</th>\n",
+ " <th>ktn</th>\n",
+ " <th>akl</th>\n",
+ " <th>sex</th>\n",
+ " <th>fallklasse_3</th>\n",
+ " <th>pttoddat</th>\n",
+ " <th>pttod_1</th>\n",
+ " <th>gender</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>2020-02-24</td>\n",
+ " <td>TI</td>\n",
+ " <td>70 - 79</td>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0</td>\n",
+ " <td>male</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>2020-02-25</td>\n",
+ " <td>AG</td>\n",
+ " <td>20 - 29</td>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0</td>\n",
+ " <td>male</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>2020-02-26</td>\n",
+ " <td>BL</td>\n",
+ " <td>20 - 29</td>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0</td>\n",
+ " <td>male</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>2020-02-26</td>\n",
+ " <td>BS</td>\n",
+ " <td>20 - 29</td>\n",
+ " <td>2</td>\n",
+ " <td>1</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0</td>\n",
+ " <td>female</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>2020-02-26</td>\n",
+ " <td>GE</td>\n",
+ " <td>20 - 29</td>\n",
+ " <td>1</td>\n",
+ " <td>1</td>\n",
+ " <td>NaN</td>\n",
+ " <td>0</td>\n",
+ " <td>male</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " replikation_dt fall_dt ktn akl sex fallklasse_3 pttoddat \\\n",
+ "0 2020-08-09 07:41:29 2020-02-24 TI 70 - 79 1 1 NaN \n",
+ "1 2020-08-09 07:41:29 2020-02-25 AG 20 - 29 1 1 NaN \n",
+ "2 2020-08-09 07:41:29 2020-02-26 BL 20 - 29 1 1 NaN \n",
+ "3 2020-08-09 07:41:29 2020-02-26 BS 20 - 29 2 1 NaN \n",
+ "4 2020-08-09 07:41:29 2020-02-26 GE 20 - 29 1 1 NaN \n",
+ "\n",
+ " pttod_1 gender \n",
+ "0 0 male \n",
+ "1 0 male \n",
+ "2 0 male \n",
+ "3 0 female \n",
+ "4 0 male "
+ ]
+ },
+ "execution_count": 8,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# Cases\n",
+ "df.head()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "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>replikation_dt</th>\n",
+ " <th>fall_dt</th>\n",
+ " <th>ktn</th>\n",
+ " <th>akl</th>\n",
+ " <th>sex</th>\n",
+ " <th>fallklasse_3</th>\n",
+ " <th>pttoddat</th>\n",
+ " <th>pttod_1</th>\n",
+ " <th>gender</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>263742</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>NaN</td>\n",
+ " <td>ZH</td>\n",
+ " <td>80+</td>\n",
+ " <td>2</td>\n",
+ " <td>0</td>\n",
+ " <td>2020-08-09</td>\n",
+ " <td>0</td>\n",
+ " <td>female</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>263743</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>NaN</td>\n",
+ " <td>ZH</td>\n",
+ " <td>80+</td>\n",
+ " <td>9</td>\n",
+ " <td>0</td>\n",
+ " <td>2020-08-09</td>\n",
+ " <td>0</td>\n",
+ " <td>unknown</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>263744</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>NaN</td>\n",
+ " <td>ZH</td>\n",
+ " <td>unknown</td>\n",
+ " <td>1</td>\n",
+ " <td>0</td>\n",
+ " <td>2020-08-09</td>\n",
+ " <td>0</td>\n",
+ " <td>male</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>263745</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>NaN</td>\n",
+ " <td>ZH</td>\n",
+ " <td>unknown</td>\n",
+ " <td>2</td>\n",
+ " <td>0</td>\n",
+ " <td>2020-08-09</td>\n",
+ " <td>0</td>\n",
+ " <td>female</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>263746</th>\n",
+ " <td>2020-08-09 07:41:29</td>\n",
+ " <td>NaN</td>\n",
+ " <td>ZH</td>\n",
+ " <td>unknown</td>\n",
+ " <td>9</td>\n",
+ " <td>0</td>\n",
+ " <td>2020-08-09</td>\n",
+ " <td>0</td>\n",
+ " <td>unknown</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " replikation_dt fall_dt ktn akl sex fallklasse_3 \\\n",
+ "263742 2020-08-09 07:41:29 NaN ZH 80+ 2 0 \n",
+ "263743 2020-08-09 07:41:29 NaN ZH 80+ 9 0 \n",
+ "263744 2020-08-09 07:41:29 NaN ZH unknown 1 0 \n",
+ "263745 2020-08-09 07:41:29 NaN ZH unknown 2 0 \n",
+ "263746 2020-08-09 07:41:29 NaN ZH unknown 9 0 \n",
+ "\n",
+ " pttoddat pttod_1 gender \n",
+ "263742 2020-08-09 0 female \n",
+ "263743 2020-08-09 0 unknown \n",
+ "263744 2020-08-09 0 male \n",
+ "263745 2020-08-09 0 female \n",
+ "263746 2020-08-09 0 unknown "
+ ]
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# Deaths\n",
+ "df.tail()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "## BAG email answer about metadata\n",
+ "\n",
+ "“La variable \"fallklasse_3\" correspond au nombre de cas pour une combinaison spécifique de date, canton, groupe d'âge et sexe (\"fallklasse_3\" sont les cas confirmés en laboratoire). Pour les décès, vous devez consulter la colonne pttod_1 qui indique le nombre de décès pour chaque combinaison spécifique de variables.â€\n",
+ "\n",
+ "Also:\n",
+ "* fall_dt = date of case (TODO: ask BAG if this is date of lab confirmation or date of infection)\n",
+ "* fallklasse_3 = confirmed case\n",
+ "* pttodat = date of death\n",
+ "* pttod_1 = death\n",
+ "\n",
+ "There’s now a file called “Variabeldokuâ€Â containing metadata: [Beschreibung der Variablen (XLS, 14 kB, 05.08.2020)](https://www.bag.admin.ch/dam/bag/de/dokumente/mt/k-und-i/aktuelle-ausbrueche-pandemien/2019-nCoV/variablendoku-dashboard.xlsx.download.xlsx/Variablendoku_dashboard.xlsx)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "2020-08-09 07:41:29 263747\n",
+ "Name: replikation_dt, dtype: int64"
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# “replikation†column seems to contain last file update\n",
+ "df['replikation_dt'].value_counts()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "df.columns = ['replikation_dt', 'case_date', 'canton', 'age', 'sex', 'cases',\n",
+ " 'death_date', 'deaths', 'gender']"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Resample"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Get rid of age and sex for a simple case per day per canton output\n",
+ "df_cases = pd.pivot_table(df[df['cases'] > 0], index='case_date', columns='canton', values='cases', aggfunc='sum')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "# Same for deaths\n",
+ "df_deaths = pd.pivot_table(df[df['deaths'] > 0], index='death_date', columns='canton', values='deaths', aggfunc='sum')"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 36,
+ "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>canton</th>\n",
+ " <th>AG</th>\n",
+ " <th>AI</th>\n",
+ " <th>AR</th>\n",
+ " <th>BE</th>\n",
+ " <th>BL</th>\n",
+ " <th>BS</th>\n",
+ " <th>FL</th>\n",
+ " <th>FR</th>\n",
+ " <th>GE</th>\n",
+ " <th>GL</th>\n",
+ " <th>...</th>\n",
+ " <th>SH</th>\n",
+ " <th>SO</th>\n",
+ " <th>SZ</th>\n",
+ " <th>TG</th>\n",
+ " <th>TI</th>\n",
+ " <th>UR</th>\n",
+ " <th>VD</th>\n",
+ " <th>VS</th>\n",
+ " <th>ZG</th>\n",
+ " <th>ZH</th>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>case_date</th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " <th></th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>2020-02-24</th>\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",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>...</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</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>2020-02-25</th>\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",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>...</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",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2020-02-26</th>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>1.0</td>\n",
+ " <td>1.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>1.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>...</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>1.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>1.0</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2020-02-27</th>\n",
+ " <td>NaN</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>3.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>...</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>3.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>1.0</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2020-02-28</th>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>2.0</td>\n",
+ " <td>2.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " <td>5.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>...</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>1.0</td>\n",
+ " <td>NaN</td>\n",
+ " <td>NaN</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "<p>5 rows × 27 columns</p>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ "canton AG AI AR BE BL BS FL FR GE GL ... SH SO SZ TG \\\n",
+ "case_date ... \n",
+ "2020-02-24 NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN \n",
+ "2020-02-25 1.0 NaN NaN NaN NaN NaN NaN NaN NaN NaN ... NaN NaN NaN NaN \n",
+ "2020-02-26 NaN NaN NaN NaN 1.0 1.0 NaN NaN 1.0 NaN ... NaN NaN NaN NaN \n",
+ "2020-02-27 NaN NaN NaN 1.0 NaN NaN NaN NaN 3.0 NaN ... NaN NaN NaN NaN \n",
+ "2020-02-28 NaN NaN NaN NaN 2.0 2.0 NaN NaN 5.0 NaN ... NaN NaN NaN NaN \n",
+ "\n",
+ "canton TI UR VD VS ZG ZH \n",
+ "case_date \n",
+ "2020-02-24 1.0 NaN NaN NaN NaN NaN \n",
+ "2020-02-25 NaN NaN NaN NaN NaN NaN \n",
+ "2020-02-26 NaN NaN 1.0 NaN NaN 1.0 \n",
+ "2020-02-27 3.0 NaN NaN NaN NaN 1.0 \n",
+ "2020-02-28 NaN NaN NaN 1.0 NaN NaN \n",
+ "\n",
+ "[5 rows x 27 columns]"
+ ]
+ },
+ "execution_count": 36,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "df_cases.head()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {},
+ "source": [
+ "# Plot"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 55,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "['SG', 'BS', 'FR', 'AG', 'VS', 'BE', 'TI', 'ZH', 'GE', 'VD']"
+ ]
+ },
+ "execution_count": 55,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "top_cantons = df_cases.sum().sort_values().tail(10).index.tolist()\n",
+ "top_cantons"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 62,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-17e18b93356148d5be825724f868858f\"></div>\n",
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+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
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+ "\n",
+ " function loadScript(lib) {\n",
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+ " s.onload = () => resolve(paths[lib]);\n",
+ " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
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+ "\n",
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+ " throw err;\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",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
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\"value\": 26.0}, {\"case_date\": \"2020-08-02T00:00:00\", \"canton\": \"VD\", \"value\": 15.0}, {\"case_date\": \"2020-08-03T00:00:00\", \"canton\": \"VD\", \"value\": 21.0}, {\"case_date\": \"2020-08-04T00:00:00\", \"canton\": \"VD\", \"value\": 14.0}, {\"case_date\": \"2020-08-05T00:00:00\", \"canton\": \"VD\", \"value\": 19.0}, {\"case_date\": \"2020-08-06T00:00:00\", \"canton\": \"VD\", \"value\": 17.0}, {\"case_date\": \"2020-08-07T00:00:00\", \"canton\": \"VD\", \"value\": 21.0}, {\"case_date\": \"2020-08-08T00:00:00\", \"canton\": \"VD\", \"value\": 7.0}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.Chart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Source: \n",
+ " <a href=\"https://www.bag.admin.ch/bag/en/home/krankheiten/ausbrueche-epidemien-pandemien/aktuelle-ausbrueche-epidemien/novel-cov/situation-schweiz-und-international.html\">Federal Office of Public Health FOPH</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\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": [
+ "data = df_cases[top_cantons].reset_index().melt('case_date')\n",
+ "chart = alt.Chart(data).mark_line().encode(\n",
+ " x=alt.Y('case_date', axis=alt.Axis(title='Date')),\n",
+ " y=alt.Y('value', axis=alt.Axis(title='Confirmed cases')),\n",
+ " color='canton'\n",
+ ").properties(\n",
+ " height=200,\n",
+ " width=600\n",
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 47,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "df_cases.index = pd.to_datetime(df_cases.index)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 64,
+ "metadata": {},
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-4ebcaea1a1cc419cb7a3d47de534d79b\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-4ebcaea1a1cc419cb7a3d47de534d79b\");\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: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}}, \"data\": {\"name\": \"data-6d46ff527c4f5524a8fa001fa3c4447a\"}, \"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"canton\"}, \"x\": {\"type\": \"temporal\", \"axis\": {\"title\": \"Date\"}, \"field\": \"case_date\"}, \"y\": {\"type\": \"quantitative\", \"axis\": {\"title\": \"Confirmed cases\"}, \"field\": \"value\"}}, \"height\": 200, \"width\": 600, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-6d46ff527c4f5524a8fa001fa3c4447a\": [{\"case_date\": \"2020-02-24T00:00:00\", \"canton\": \"SG\", \"value\": 0.0}, {\"case_date\": \"2020-02-25T00:00:00\", \"canton\": \"SG\", \"value\": 0.0}, {\"case_date\": \"2020-02-26T00:00:00\", \"canton\": \"SG\", \"value\": 0.0}, {\"case_date\": \"2020-02-27T00:00:00\", \"canton\": \"SG\", \"value\": 0.0}, {\"case_date\": \"2020-02-28T00:00:00\", \"canton\": \"SG\", \"value\": 0.0}, {\"case_date\": \"2020-02-29T00:00:00\", \"canton\": \"SG\", \"value\": 0.0}, {\"case_date\": \"2020-03-01T00:00:00\", \"canton\": \"SG\", \"value\": 0.0}, {\"case_date\": \"2020-03-02T00:00:00\", \"canton\": \"SG\", \"value\": 0.14285714285714285}, {\"case_date\": \"2020-03-03T00:00:00\", \"canton\": \"SG\", \"value\": 0.14285714285714285}, {\"case_date\": \"2020-03-04T00:00:00\", \"canton\": \"SG\", \"value\": 0.14285714285714285}, {\"case_date\": \"2020-03-05T00:00:00\", \"canton\": \"SG\", \"value\": 0.14285714285714285}, {\"case_date\": \"2020-03-06T00:00:00\", \"canton\": \"SG\", \"value\": 0.5714285714285714}, {\"case_date\": \"2020-03-07T00:00:00\", \"canton\": \"SG\", \"value\": 0.5714285714285714}, {\"case_date\": \"2020-03-08T00:00:00\", \"canton\": \"SG\", \"value\": 0.7142857142857143}, {\"case_date\": \"2020-03-09T00:00:00\", \"canton\": \"SG\", \"value\": 1.7142857142857142}, {\"case_date\": \"2020-03-10T00:00:00\", \"canton\": \"SG\", \"value\": 1.8571428571428572}, 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{\"case_date\": \"2020-03-13T00:00:00\", \"canton\": \"VD\", \"value\": 49.0}, {\"case_date\": \"2020-03-14T00:00:00\", \"canton\": \"VD\", \"value\": 62.714285714285715}, {\"case_date\": \"2020-03-15T00:00:00\", \"canton\": \"VD\", \"value\": 74.42857142857143}, {\"case_date\": \"2020-03-16T00:00:00\", \"canton\": \"VD\", \"value\": 103.14285714285714}, {\"case_date\": \"2020-03-17T00:00:00\", \"canton\": \"VD\", \"value\": 132.85714285714286}, {\"case_date\": \"2020-03-18T00:00:00\", \"canton\": \"VD\", \"value\": 160.85714285714286}, {\"case_date\": \"2020-03-19T00:00:00\", \"canton\": \"VD\", \"value\": 181.0}, {\"case_date\": \"2020-03-20T00:00:00\", \"canton\": \"VD\", \"value\": 201.71428571428572}, {\"case_date\": \"2020-03-21T00:00:00\", \"canton\": \"VD\", \"value\": 203.71428571428572}, {\"case_date\": \"2020-03-22T00:00:00\", \"canton\": \"VD\", \"value\": 205.57142857142858}, {\"case_date\": \"2020-03-23T00:00:00\", \"canton\": \"VD\", \"value\": 216.14285714285714}, {\"case_date\": \"2020-03-24T00:00:00\", \"canton\": \"VD\", \"value\": 219.57142857142858}, {\"case_date\": \"2020-03-25T00:00:00\", \"canton\": \"VD\", \"value\": 208.71428571428572}, {\"case_date\": \"2020-03-26T00:00:00\", \"canton\": \"VD\", \"value\": 207.28571428571428}, {\"case_date\": \"2020-03-27T00:00:00\", \"canton\": \"VD\", \"value\": 206.71428571428572}, {\"case_date\": \"2020-03-28T00:00:00\", \"canton\": \"VD\", \"value\": 208.28571428571428}, {\"case_date\": \"2020-03-29T00:00:00\", \"canton\": \"VD\", \"value\": 205.85714285714286}, {\"case_date\": \"2020-03-30T00:00:00\", \"canton\": \"VD\", \"value\": 192.0}, {\"case_date\": \"2020-03-31T00:00:00\", \"canton\": \"VD\", \"value\": 176.28571428571428}, {\"case_date\": \"2020-04-01T00:00:00\", \"canton\": \"VD\", \"value\": 170.42857142857142}, {\"case_date\": \"2020-04-02T00:00:00\", \"canton\": \"VD\", \"value\": 160.42857142857142}, {\"case_date\": \"2020-04-03T00:00:00\", \"canton\": \"VD\", \"value\": 146.0}, {\"case_date\": \"2020-04-04T00:00:00\", \"canton\": \"VD\", \"value\": 137.42857142857142}, {\"case_date\": \"2020-04-05T00:00:00\", \"canton\": \"VD\", \"value\": 130.71428571428572}, {\"case_date\": \"2020-04-06T00:00:00\", \"canton\": \"VD\", \"value\": 117.14285714285714}, {\"case_date\": \"2020-04-07T00:00:00\", \"canton\": \"VD\", \"value\": 105.71428571428571}, {\"case_date\": \"2020-04-08T00:00:00\", \"canton\": \"VD\", \"value\": 97.28571428571429}, {\"case_date\": \"2020-04-09T00:00:00\", \"canton\": \"VD\", \"value\": 91.71428571428571}, {\"case_date\": \"2020-04-10T00:00:00\", \"canton\": \"VD\", \"value\": 79.14285714285714}, {\"case_date\": \"2020-04-11T00:00:00\", \"canton\": \"VD\", \"value\": 74.57142857142857}, {\"case_date\": \"2020-04-12T00:00:00\", \"canton\": \"VD\", \"value\": 74.28571428571429}, {\"case_date\": \"2020-04-13T00:00:00\", \"canton\": \"VD\", \"value\": 63.57142857142857}, {\"case_date\": \"2020-04-14T00:00:00\", \"canton\": \"VD\", \"value\": 61.857142857142854}, {\"case_date\": \"2020-04-15T00:00:00\", \"canton\": \"VD\", \"value\": 55.714285714285715}, {\"case_date\": \"2020-04-16T00:00:00\", \"canton\": \"VD\", \"value\": 46.142857142857146}, {\"case_date\": \"2020-04-17T00:00:00\", \"canton\": \"VD\", \"value\": 43.857142857142854}, {\"case_date\": \"2020-04-18T00:00:00\", \"canton\": \"VD\", \"value\": 40.857142857142854}, {\"case_date\": \"2020-04-19T00:00:00\", \"canton\": \"VD\", \"value\": 36.857142857142854}, {\"case_date\": \"2020-04-20T00:00:00\", \"canton\": \"VD\", \"value\": 35.285714285714285}, {\"case_date\": \"2020-04-21T00:00:00\", \"canton\": \"VD\", \"value\": 29.857142857142858}, {\"case_date\": \"2020-04-22T00:00:00\", \"canton\": \"VD\", \"value\": 25.714285714285715}, {\"case_date\": \"2020-04-23T00:00:00\", \"canton\": \"VD\", \"value\": 25.857142857142858}, {\"case_date\": \"2020-04-24T00:00:00\", \"canton\": \"VD\", \"value\": 24.285714285714285}, {\"case_date\": \"2020-04-25T00:00:00\", \"canton\": \"VD\", \"value\": 23.428571428571427}, {\"case_date\": \"2020-04-26T00:00:00\", \"canton\": \"VD\", \"value\": 23.142857142857142}, {\"case_date\": \"2020-04-27T00:00:00\", \"canton\": \"VD\", \"value\": 21.0}, {\"case_date\": \"2020-04-28T00:00:00\", \"canton\": \"VD\", \"value\": 19.714285714285715}, {\"case_date\": \"2020-04-29T00:00:00\", \"canton\": \"VD\", \"value\": 18.714285714285715}, {\"case_date\": \"2020-04-30T00:00:00\", \"canton\": \"VD\", \"value\": 16.142857142857142}, {\"case_date\": \"2020-05-01T00:00:00\", \"canton\": \"VD\", \"value\": 15.428571428571429}, {\"case_date\": \"2020-05-02T00:00:00\", \"canton\": \"VD\", \"value\": 14.857142857142858}, {\"case_date\": \"2020-05-03T00:00:00\", \"canton\": \"VD\", \"value\": 14.285714285714286}, {\"case_date\": \"2020-05-04T00:00:00\", \"canton\": \"VD\", \"value\": 13.0}, {\"case_date\": \"2020-05-05T00:00:00\", \"canton\": \"VD\", \"value\": 11.285714285714286}, {\"case_date\": \"2020-05-06T00:00:00\", 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\"2020-05-28T00:00:00\", \"canton\": \"VD\", \"value\": 2.857142857142857}, {\"case_date\": \"2020-05-29T00:00:00\", \"canton\": \"VD\", \"value\": 2.7142857142857144}, {\"case_date\": \"2020-05-30T00:00:00\", \"canton\": \"VD\", \"value\": 2.0}, {\"case_date\": \"2020-05-31T00:00:00\", \"canton\": \"VD\", \"value\": 1.8571428571428572}, {\"case_date\": \"2020-06-01T00:00:00\", \"canton\": \"VD\", \"value\": 1.8571428571428572}, {\"case_date\": \"2020-06-02T00:00:00\", \"canton\": \"VD\", \"value\": 2.0}, {\"case_date\": \"2020-06-03T00:00:00\", \"canton\": \"VD\", \"value\": 2.0}, {\"case_date\": \"2020-06-04T00:00:00\", \"canton\": \"VD\", \"value\": 2.0}, {\"case_date\": \"2020-06-05T00:00:00\", \"canton\": \"VD\", \"value\": 1.8571428571428572}, {\"case_date\": \"2020-06-06T00:00:00\", \"canton\": \"VD\", \"value\": 2.0}, {\"case_date\": \"2020-06-07T00:00:00\", \"canton\": \"VD\", \"value\": 2.142857142857143}, {\"case_date\": \"2020-06-08T00:00:00\", \"canton\": \"VD\", 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3.5714285714285716}, {\"case_date\": \"2020-06-20T00:00:00\", \"canton\": \"VD\", \"value\": 3.857142857142857}, {\"case_date\": \"2020-06-21T00:00:00\", \"canton\": \"VD\", \"value\": 4.0}, {\"case_date\": \"2020-06-22T00:00:00\", \"canton\": \"VD\", \"value\": 5.142857142857143}, {\"case_date\": \"2020-06-23T00:00:00\", \"canton\": \"VD\", \"value\": 5.0}, {\"case_date\": \"2020-06-24T00:00:00\", \"canton\": \"VD\", \"value\": 5.714285714285714}, {\"case_date\": \"2020-06-25T00:00:00\", \"canton\": \"VD\", \"value\": 5.857142857142857}, {\"case_date\": \"2020-06-26T00:00:00\", \"canton\": \"VD\", \"value\": 5.857142857142857}, {\"case_date\": \"2020-06-27T00:00:00\", \"canton\": \"VD\", \"value\": 5.857142857142857}, {\"case_date\": \"2020-06-28T00:00:00\", \"canton\": \"VD\", \"value\": 6.714285714285714}, {\"case_date\": \"2020-06-29T00:00:00\", \"canton\": \"VD\", \"value\": 7.428571428571429}, {\"case_date\": \"2020-06-30T00:00:00\", \"canton\": \"VD\", \"value\": 8.714285714285714}, {\"case_date\": \"2020-07-01T00:00:00\", \"canton\": \"VD\", \"value\": 8.714285714285714}, {\"case_date\": \"2020-07-02T00:00:00\", \"canton\": \"VD\", \"value\": 12.0}, {\"case_date\": \"2020-07-03T00:00:00\", \"canton\": \"VD\", \"value\": 13.0}, {\"case_date\": \"2020-07-04T00:00:00\", \"canton\": \"VD\", \"value\": 13.142857142857142}, {\"case_date\": \"2020-07-05T00:00:00\", \"canton\": \"VD\", \"value\": 13.0}, {\"case_date\": \"2020-07-06T00:00:00\", \"canton\": \"VD\", \"value\": 12.571428571428571}, {\"case_date\": \"2020-07-07T00:00:00\", \"canton\": \"VD\", \"value\": 12.571428571428571}, {\"case_date\": \"2020-07-08T00:00:00\", \"canton\": \"VD\", \"value\": 13.285714285714286}, {\"case_date\": \"2020-07-09T00:00:00\", \"canton\": \"VD\", \"value\": 11.285714285714286}, {\"case_date\": \"2020-07-10T00:00:00\", \"canton\": \"VD\", \"value\": 11.428571428571429}, {\"case_date\": \"2020-07-11T00:00:00\", \"canton\": \"VD\", \"value\": 12.142857142857142}, {\"case_date\": \"2020-07-12T00:00:00\", \"canton\": \"VD\", \"value\": 12.0}, {\"case_date\": \"2020-07-13T00:00:00\", \"canton\": \"VD\", \"value\": 12.142857142857142}, {\"case_date\": \"2020-07-14T00:00:00\", \"canton\": \"VD\", \"value\": 12.571428571428571}, {\"case_date\": \"2020-07-15T00:00:00\", \"canton\": \"VD\", \"value\": 13.0}, {\"case_date\": \"2020-07-16T00:00:00\", \"canton\": \"VD\", \"value\": 13.285714285714286}, {\"case_date\": \"2020-07-17T00:00:00\", \"canton\": \"VD\", \"value\": 13.571428571428571}, {\"case_date\": \"2020-07-18T00:00:00\", \"canton\": \"VD\", \"value\": 13.857142857142858}, {\"case_date\": \"2020-07-19T00:00:00\", \"canton\": \"VD\", \"value\": 13.857142857142858}, {\"case_date\": \"2020-07-20T00:00:00\", \"canton\": \"VD\", \"value\": 13.857142857142858}, {\"case_date\": \"2020-07-21T00:00:00\", \"canton\": \"VD\", \"value\": 12.0}, {\"case_date\": \"2020-07-22T00:00:00\", \"canton\": \"VD\", \"value\": 11.0}, {\"case_date\": \"2020-07-23T00:00:00\", \"canton\": \"VD\", \"value\": 10.571428571428571}, {\"case_date\": \"2020-07-24T00:00:00\", \"canton\": \"VD\", \"value\": 10.428571428571429}, {\"case_date\": \"2020-07-25T00:00:00\", \"canton\": \"VD\", \"value\": 10.714285714285714}, {\"case_date\": \"2020-07-26T00:00:00\", \"canton\": \"VD\", \"value\": 10.714285714285714}, {\"case_date\": \"2020-07-27T00:00:00\", \"canton\": \"VD\", \"value\": 11.857142857142858}, {\"case_date\": \"2020-07-28T00:00:00\", \"canton\": \"VD\", \"value\": 15.142857142857142}, {\"case_date\": \"2020-07-29T00:00:00\", \"canton\": \"VD\", \"value\": 19.571428571428573}, {\"case_date\": \"2020-07-30T00:00:00\", \"canton\": \"VD\", \"value\": 21.285714285714285}, {\"case_date\": \"2020-07-31T00:00:00\", \"canton\": \"VD\", \"value\": 21.857142857142858}, {\"case_date\": \"2020-08-01T00:00:00\", \"canton\": \"VD\", \"value\": 23.857142857142858}, {\"case_date\": \"2020-08-02T00:00:00\", \"canton\": \"VD\", \"value\": 25.142857142857142}, {\"case_date\": \"2020-08-03T00:00:00\", \"canton\": \"VD\", \"value\": 25.0}, {\"case_date\": \"2020-08-04T00:00:00\", \"canton\": \"VD\", \"value\": 22.857142857142858}, {\"case_date\": \"2020-08-05T00:00:00\", \"canton\": \"VD\", \"value\": 19.571428571428573}, {\"case_date\": \"2020-08-06T00:00:00\", \"canton\": \"VD\", \"value\": 18.714285714285715}, {\"case_date\": \"2020-08-07T00:00:00\", \"canton\": \"VD\", \"value\": 19.0}, {\"case_date\": \"2020-08-08T00:00:00\", \"canton\": \"VD\", \"value\": 16.285714285714285}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.Chart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Source: \n",
+ " <a href=\"https://www.bag.admin.ch/bag/en/home/krankheiten/ausbrueche-epidemien-pandemien/aktuelle-ausbrueche-epidemien/novel-cov/situation-schweiz-und-international.html\">Federal Office of Public Health FOPH</a>\n",
+ "<br>\n",
+ "Analysis and Visualization:\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": [
+ "data = df_cases[top_cantons].fillna(0).rolling('7d').mean().reset_index().melt('case_date')\n",
+ "chart = alt.Chart(data).mark_line().encode(\n",
+ " x=alt.Y('case_date', axis=alt.Axis(title='Date')),\n",
+ " y=alt.Y('value', axis=alt.Axis(title='Confirmed cases')),\n",
+ " color='canton'\n",
+ ").properties(\n",
+ " height=200,\n",
+ " width=600\n",
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "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",
+ "version": "3.7.3"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
--
GitLab