From c737eb9119a0c611da355a20599622b7204dfd49 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= <rok.roskar@sdsc.ethz.ch>
Date: Tue, 28 Apr 2020 19:28:00 +0000
Subject: [PATCH] renku run --input
data/covid-19-italy/dpc-covid19-ita-regioni.csv --input
data/covid-19-us-nyt/us-counties.csv --input data/covid-19-spain/ --input
data/covid-19-ecdc/covid-19-ecdc.csv papermill
notebooks/datasets_summary.ipynb runs/dataset_summary.run.ipynb -p data_path
data/ -p atlas_path data/atlas/
---
...5990857443d0abde4c4f09ab402e_papermill.cwl | 127 ++
runs/dataset_summary.run.ipynb | 1305 +++++++++++++++++
2 files changed, 1432 insertions(+)
create mode 100644 .renku/workflow/696b5990857443d0abde4c4f09ab402e_papermill.cwl
create mode 100644 runs/dataset_summary.run.ipynb
diff --git a/.renku/workflow/696b5990857443d0abde4c4f09ab402e_papermill.cwl b/.renku/workflow/696b5990857443d0abde4c4f09ab402e_papermill.cwl
new file mode 100644
index 000000000..26b8fb809
--- /dev/null
+++ b/.renku/workflow/696b5990857443d0abde4c4f09ab402e_papermill.cwl
@@ -0,0 +1,127 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default:
+ class: File
+ path: ../../notebooks/datasets_summary.ipynb
+ inputBinding:
+ position: 1
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_10:
+ default:
+ class: File
+ path: ../../data/covid-19-ecdc/covid-19-ecdc.csv
+ streamable: false
+ type: File
+ input_2:
+ default: runs/dataset_summary.run.ipynb
+ inputBinding:
+ position: 2
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_3:
+ default: data_path
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_5:
+ default: atlas_path
+ inputBinding:
+ position: 5
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_6:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/atlas
+ inputBinding:
+ position: 6
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: Directory
+ input_7:
+ default:
+ class: File
+ path: ../../data/covid-19-italy/dpc-covid19-ita-regioni.csv
+ streamable: false
+ type: File
+ input_8:
+ default:
+ class: File
+ path: ../../data/covid-19-us-nyt/us-counties.csv
+ streamable: false
+ type: File
+ input_9:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19-spain
+ streamable: false
+ type: Directory
+outputs:
+ output_0:
+ outputBinding:
+ glob: $(inputs.input_2)
+ streamable: false
+ type: File
+permanentFailCodes: []
+requirements:
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: '$({"listing": [], "class": "Directory"})'
+ entryname: runs
+ writable: true
+ - entry: $(inputs.input_1)
+ entryname: notebooks/datasets_summary.ipynb
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data
+ writable: false
+ - entry: $(inputs.input_6)
+ entryname: data/atlas
+ writable: false
+ - entry: $(inputs.input_7)
+ entryname: data/covid-19-italy/dpc-covid19-ita-regioni.csv
+ writable: false
+ - entry: $(inputs.input_8)
+ entryname: data/covid-19-us-nyt/us-counties.csv
+ writable: false
+ - entry: $(inputs.input_9)
+ entryname: data/covid-19-spain
+ writable: false
+ - entry: $(inputs.input_10)
+ entryname: data/covid-19-ecdc/covid-19-ecdc.csv
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/runs/dataset_summary.run.ipynb b/runs/dataset_summary.run.ipynb
new file mode 100644
index 000000000..6a00d77cd
--- /dev/null
+++ b/runs/dataset_summary.run.ipynb
@@ -0,0 +1,1305 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "papermill": {
+ "duration": 0.063933,
+ "end_time": "2020-04-28T19:27:53.765279",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:53.701346",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "%load_ext autoreload\n",
+ "%autoreload 2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "papermill": {
+ "duration": 0.048917,
+ "end_time": "2020-04-28T19:27:53.836867",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:53.787950",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "from IPython.display import display, HTML\n",
+ "renkulab_credits = HTML(\"\"\"<p style=\"font-size: smaller\">Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">\n",
+ " Covid-19 Public Data Collaboration Project @ renkulab.io\n",
+ " </a>\n",
+ " </p>\n",
+ "\"\"\")\n",
+ "ecdc_credits=HTML('''\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide\">ECDC</a>\n",
+ "</p>\n",
+ "'''\n",
+ ")\n",
+ "all_credits=HTML(\"\"\"\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide\">ECDC</a>, \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, \n",
+ " <a href=\"https://github.com/nytimes/covid-19-data\">The New York Times</a>, \n",
+ " <a href=\"https://github.com/datadista/datasets\">Datadista</a>.\n",
+ "</p>\n",
+ "\"\"\")"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.009844,
+ "end_time": "2020-04-28T19:27:53.856840",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:53.846996",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "# Global and Regional Covid-19 Case Count Data\n",
+ "\n",
+ "In this project we collect data about the ongoing Covid-19 pandemic from a variety of sources. Some aggregate worldwide country-level statistics while others provide fine-grained data about regions of individual countries. \n",
+ "\n",
+ "Here we summarize some of the available data using the simple standardized views we have built for these datasets, which allow us to use the same analysis tools across the heterogeneous datasets. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "papermill": {
+ "duration": 0.448861,
+ "end_time": "2020-04-28T19:27:54.316818",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:53.867957",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Standard python imports - we will be using pandas for data wrangling and altair for visualization\n",
+ "from datetime import datetime\n",
+ "from pathlib import Path\n",
+ "\n",
+ "import altair as alt\n",
+ "import pandas as pd"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "metadata": {
+ "papermill": {
+ "duration": 0.055302,
+ "end_time": "2020-04-28T19:27:54.398557",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:54.343255",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Importing our custom tools for the datasets in this repository. \n",
+ "from covid_19_utils import helper, plotting\n",
+ "from covid_19_utils.converters import CaseConverter"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "papermill": {
+ "duration": 0.039177,
+ "end_time": "2020-04-28T19:27:54.456336",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:54.417159",
+ "status": "completed"
+ },
+ "tags": [
+ "parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "data_path = \"../data\"\n",
+ "atlas_path = \"../data/atlas\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "papermill": {
+ "duration": 0.047617,
+ "end_time": "2020-04-28T19:27:54.523422",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:54.475805",
+ "status": "completed"
+ },
+ "tags": [
+ "injected-parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "# Parameters\n",
+ "data_path = \"data/\"\n",
+ "atlas_path = \"data/atlas/\"\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "papermill": {
+ "duration": 0.047258,
+ "end_time": "2020-04-28T19:27:54.587783",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:54.540525",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Instantiating the CaseConverter to read in the data.\n",
+ "# It takes a path to the atlas dataset as an argument - the atlas holds various population and country metadata data. \n",
+ "converter = CaseConverter(atlas_path)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.01167,
+ "end_time": "2020-04-28T19:27:54.622339",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:54.610669",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## Global deaths attributed to Covid-19\n",
+ "\n",
+ "How deadly has the pandemic been over the past few months? Where has it proven to be the deadliest? We investigate the data collected by the [European Center for Disease Prevention and Control](https://www.ecdc.europa.eu/en) to gain some basic understanding of these questions. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "papermill": {
+ "duration": 0.356898,
+ "end_time": "2020-04-28T19:27:54.989486",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:54.632588",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# read in the data from the European Center for Disease Prevention and Control\n",
+ "global_df = converter.read_convert(Path(data_path) / \"covid-19-ecdc\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "papermill": {
+ "duration": 0.12036,
+ "end_time": "2020-04-28T19:27:55.133994",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:55.013634",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-911b70f6ccb84880901aa2ba6b8e9e20\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-911b70f6ccb84880901aa2ba6b8e9e20\");\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",
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+ " \"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",
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+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
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{\"date\": \"2020-03-19T00:00:00\", \"deceased_100k\": 52.13768569150822, \"deceased_daily\": 951, \"deceased\": 8835, \"positive_100k\": 1198.8613004195056, \"positive_daily\": 18306, \"positive\": 212445}, {\"date\": \"2020-03-20T00:00:00\", \"deceased_100k\": 54.803276206731084, \"deceased_daily\": 1041, \"deceased\": 9876, \"positive_100k\": 1618.3404071998007, \"positive_daily\": 29225, \"positive\": 241674}, {\"date\": \"2020-03-21T00:00:00\", \"deceased_100k\": 59.35605195390208, \"deceased_daily\": 1366, \"deceased\": 11242, \"positive_100k\": 1905.3894390739124, \"positive_daily\": 28742, \"positive\": 270411}, {\"date\": \"2020-03-22T00:00:00\", \"deceased_100k\": 81.84219084525584, \"deceased_daily\": 1700, \"deceased\": 12942, \"positive_100k\": 2134.8343082823612, \"positive_daily\": 34119, \"positive\": 304530}, {\"date\": \"2020-03-23T00:00:00\", \"deceased_100k\": 85.20559876654839, \"deceased_daily\": 1654, \"deceased\": 14596, \"positive_100k\": 2472.359791207972, 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15693.337209080066, \"positive_daily\": 76607, \"positive\": 2744048}, {\"date\": \"2020-04-26T00:00:00\", \"deceased_100k\": 752.6075883938273, \"deceased_daily\": 5929, \"deceased\": 178784, \"positive_100k\": 15502.454575160647, \"positive_daily\": 99968, \"positive\": 2624252}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide\">ECDC</a>\n",
+ "</p>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "<p style=\"font-size: smaller\">Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">\n",
+ " Covid-19 Public Data Collaboration Project @ renkulab.io\n",
+ " </a>\n",
+ " </p>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# Set a start date of Feb 1st and plot the daily deaths globally\n",
+ "start_date = datetime.fromisoformat('2020-02-01')\n",
+ "global_daily_totals = global_df.groupby('date').sum().reset_index()\n",
+ "\n",
+ "# basic chart\n",
+ "base = alt.Chart(global_daily_totals.loc[global_daily_totals.date >= start_date])\n",
+ "\n",
+ "chart = base.mark_line().encode(\n",
+ " x=alt.X('date', title='Date'),\n",
+ " y=alt.Y('deceased_daily', title='Daily deaths')\n",
+ ")\n",
+ "\n",
+ "# 7-day mean - we use the altair window function to compute this directly\n",
+ "running_mean = base.transform_window(\n",
+ " mean_deceased='mean(deceased_daily)',\n",
+ " frame=[-3, 3],\n",
+ ").mark_area(opacity=0.3, color='orange').encode(\n",
+ " x='date',\n",
+ " y='mean_deceased:Q'\n",
+ ")\n",
+ "\n",
+ "# combine the two charts together and set the size and title\n",
+ "combined = (\n",
+ " chart +\n",
+ " running_mean +\n",
+ " running_mean.mark_line(color='orange')\n",
+ ").properties(\n",
+ " width=600,\n",
+ " height=350,\n",
+ " title=\"Daily global deaths and 7-day mean\"\n",
+ ")\n",
+ "\n",
+ "display(combined)\n",
+ "display(ecdc_credits)\n",
+ "display(renkulab_credits)"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.011446,
+ "end_time": "2020-04-28T19:27:55.164637",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:55.153191",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "### Top ten countries by total number of deaths attributed to Covid-19"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "papermill": {
+ "duration": 0.07246,
+ "end_time": "2020-04-28T19:27:55.254471",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:55.182011",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Sort countries by their total deaths \n",
+ "country_death_sort = global_df.groupby(\n",
+ " \"country_label\"\n",
+ ")['deceased'].max().sort_values(\n",
+ " ascending=False\n",
+ ").index.to_list()"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "papermill": {
+ "duration": 0.074552,
+ "end_time": "2020-04-28T19:27:55.354194",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:55.279642",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "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>Country</th>\n",
+ " <th>Deaths</th>\n",
+ " <th>Deaths per 100k</th>\n",
+ " <th>Positive cases</th>\n",
+ " <th>Positive cases per 100k</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <th>0</th>\n",
+ " <td>United States of America</td>\n",
+ " <td>53189</td>\n",
+ " <td>16.257425</td>\n",
+ " <td>939053</td>\n",
+ " <td>287.025206</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>1</th>\n",
+ " <td>Italy</td>\n",
+ " <td>26384</td>\n",
+ " <td>43.659507</td>\n",
+ " <td>195351</td>\n",
+ " <td>323.261381</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>2</th>\n",
+ " <td>France</td>\n",
+ " <td>22614</td>\n",
+ " <td>33.758666</td>\n",
+ " <td>124114</td>\n",
+ " <td>185.280051</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>3</th>\n",
+ " <td>United Kingdom</td>\n",
+ " <td>20319</td>\n",
+ " <td>30.559946</td>\n",
+ " <td>148377</td>\n",
+ " <td>223.160252</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>4</th>\n",
+ " <td>Belgium</td>\n",
+ " <td>6917</td>\n",
+ " <td>60.558211</td>\n",
+ " <td>45325</td>\n",
+ " <td>396.819560</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>5</th>\n",
+ " <td>Iran</td>\n",
+ " <td>5650</td>\n",
+ " <td>6.907068</td>\n",
+ " <td>89328</td>\n",
+ " <td>109.202575</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>6</th>\n",
+ " <td>Germany</td>\n",
+ " <td>5640</td>\n",
+ " <td>6.801087</td>\n",
+ " <td>154175</td>\n",
+ " <td>185.914462</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>7</th>\n",
+ " <td>China</td>\n",
+ " <td>4636</td>\n",
+ " <td>0.332871</td>\n",
+ " <td>83909</td>\n",
+ " <td>6.024786</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>8</th>\n",
+ " <td>Netherlands</td>\n",
+ " <td>4409</td>\n",
+ " <td>25.587578</td>\n",
+ " <td>37190</td>\n",
+ " <td>215.831718</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <th>9</th>\n",
+ " <td>Brazil</td>\n",
+ " <td>4016</td>\n",
+ " <td>1.917226</td>\n",
+ " <td>58509</td>\n",
+ " <td>27.932012</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "</div>"
+ ],
+ "text/plain": [
+ " Country Deaths Deaths per 100k Positive cases \\\n",
+ "0 United States of America 53189 16.257425 939053 \n",
+ "1 Italy 26384 43.659507 195351 \n",
+ "2 France 22614 33.758666 124114 \n",
+ "3 United Kingdom 20319 30.559946 148377 \n",
+ "4 Belgium 6917 60.558211 45325 \n",
+ "5 Iran 5650 6.907068 89328 \n",
+ "6 Germany 5640 6.801087 154175 \n",
+ "7 China 4636 0.332871 83909 \n",
+ "8 Netherlands 4409 25.587578 37190 \n",
+ "9 Brazil 4016 1.917226 58509 \n",
+ "\n",
+ " Positive cases per 100k \n",
+ "0 287.025206 \n",
+ "1 323.261381 \n",
+ "2 185.280051 \n",
+ "3 223.160252 \n",
+ "4 396.819560 \n",
+ "5 109.202575 \n",
+ "6 185.914462 \n",
+ "7 6.024786 \n",
+ "8 215.831718 \n",
+ "9 27.932012 "
+ ]
+ },
+ "execution_count": 11,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "# define some column translations for nicer display and print the top ten\n",
+ "columns = [\"deceased\", \"deceased_100k\", \"positive\", \"positive_100k\"]\n",
+ "pretty_print_columns = {\n",
+ " \"deceased\": \"Deaths\",\n",
+ " \"deceased_daily\": \"Daily deaths\",\n",
+ " \"deceased_100k\": \"Deaths per 100k\",\n",
+ " \"positive\": \"Positive cases\", \n",
+ " \"positive_daily\": \"Daily positive cases\",\n",
+ " \"positive_100k\": \"Positive cases per 100k\",\n",
+ " \"country_label\": \"Country\",\n",
+ " \"county_state\": \"County, State\",\n",
+ " \"region_label\": \"Region\"\n",
+ " }\n",
+ "\n",
+ "# global data sorted by cumulative deaths\n",
+ "global_sorted = global_df.set_index([\"country_label\"]).loc[country_death_sort]\n",
+ "\n",
+ "# display a table of cumulative data for the top ten countries by total deaths\n",
+ "global_sorted.loc[\n",
+ " global_sorted.date == global_sorted.date.max()\n",
+ "][columns].reset_index().rename(\n",
+ " columns=pretty_print_columns\n",
+ ")[:10]"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.011835,
+ "end_time": "2020-04-28T19:27:55.388505",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:55.376670",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## Growth of deaths in hardest-hit regions\n",
+ "\n",
+ "For the three top countries in the list above we have regional datasets - in each of those, specific regions have contributed disproportionately to the death counts in their respective countries. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "papermill": {
+ "duration": 2.911695,
+ "end_time": "2020-04-28T19:27:58.312325",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:55.400630",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# read in the regional data for the U.S., Italy and Spain\n",
+ "us_df = converter.read_convert(Path(data_path) / \"covid-19-us-nyt\")\n",
+ "spain_df = converter.read_convert(Path(data_path) / \"covid-19-spain\")\n",
+ "italy_df = converter.read_convert(Path(data_path) / \"covid-19-italy/dpc-covid19-ita-regioni.csv\")\n",
+ "\n",
+ "# In the U.S. there are counties with the same name in different states - create a unique key\n",
+ "us_df['county_state'] = us_df.apply(lambda row: f\"{row['admin2_label']}, {row['region_label']}\", axis=1)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {
+ "papermill": {
+ "duration": 0.057327,
+ "end_time": "2020-04-28T19:27:58.414073",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:58.356746",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# In each country, find the three most affected regions. \n",
+ "# Note that in these data we have two levels of sub-regions. \n",
+ "# For the U.S. data this means that \"regions\" are \"states\" and \"admin_2\" refers to \"counties\"."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {
+ "papermill": {
+ "duration": 0.067214,
+ "end_time": "2020-04-28T19:27:58.513312",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:58.446098",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# we define a simple function to return the top five \"keys\" based on a particular \"field\"\n",
+ "\n",
+ "def get_top5(df,key=\"region_label\",field=\"deceased\"):\n",
+ " \"\"\"Return the top 5 keys\"\"\"\n",
+ " return df.groupby(key).last().sort_values(by=field, ascending=False).reset_index().iloc[:5]"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {
+ "papermill": {
+ "duration": 0.187103,
+ "end_time": "2020-04-28T19:27:58.725007",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:58.537904",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <h3>\n",
+ " Cummulative deaths attributed to Covid-19 in U.S., Spain and Italy\n",
+ " </h3>\n",
+ " "
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ " <h4>United States</h4>\n",
+ " <p style=\"font-size: smaller\">(based on data from Apr. 25, 2020)</p>\n",
+ " <table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th>County, State</th>\n",
+ " <th>Deaths</th>\n",
+ " <th>Deaths per 100k</th>\n",
+ " <th>Positive cases</th>\n",
+ " <th>Positive cases per 100k</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <td>New York City, New York</td>\n",
+ " <td>11419</td>\n",
+ " <td>136.970741</td>\n",
+ " <td>155124</td>\n",
+ " <td>1860.710149</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Nassau, New York</td>\n",
+ " <td>1917</td>\n",
+ " <td>141.275414</td>\n",
+ " <td>33798</td>\n",
+ " <td>2490.780619</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Wayne, Michigan</td>\n",
+ " <td>1560</td>\n",
+ " <td>89.176336</td>\n",
+ " <td>15548</td>\n",
+ " <td>888.790820</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Cook, Illinois</td>\n",
+ " <td>1267</td>\n",
+ " <td>24.600829</td>\n",
+ " <td>29058</td>\n",
+ " <td>564.207483</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Suffolk, New York</td>\n",
+ " <td>1085</td>\n",
+ " <td>73.479566</td>\n",
+ " <td>31368</td>\n",
+ " <td>2124.338261</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "\n",
+ " <h4>Spain</h4>\n",
+ " <p style=\"font-size: smaller\">(based on data from Apr. 26, 2020)</p>\n",
+ " <table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th>Region</th>\n",
+ " <th>Deaths</th>\n",
+ " <th>Deaths per 100k</th>\n",
+ " <th>Positive cases</th>\n",
+ " <th>Positive cases per 100k</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <td>Madrid</td>\n",
+ " <td>7922.0</td>\n",
+ " <td>118.914150</td>\n",
+ " <td>62817</td>\n",
+ " <td>942.922259</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Cataluña</td>\n",
+ " <td>4566.0</td>\n",
+ " <td>59.925239</td>\n",
+ " <td>47838</td>\n",
+ " <td>627.836967</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Castilla-La Mancha</td>\n",
+ " <td>2330.0</td>\n",
+ " <td>110.618891</td>\n",
+ " <td>18995</td>\n",
+ " <td>901.805082</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Castilla y León</td>\n",
+ " <td>1666.0</td>\n",
+ " <td>68.880148</td>\n",
+ " <td>18684</td>\n",
+ " <td>772.483001</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>PaÃs Vasco</td>\n",
+ " <td>1230.0</td>\n",
+ " <td>56.741986</td>\n",
+ " <td>14315</td>\n",
+ " <td>660.375226</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ "\n",
+ " <h4>Italy</h4>\n",
+ " <p style=\"font-size: smaller\">(based on data from Apr. 26, 2020)</p>\n",
+ " <table border=\"1\" class=\"dataframe\">\n",
+ " <thead>\n",
+ " <tr style=\"text-align: right;\">\n",
+ " <th>Region</th>\n",
+ " <th>Deaths</th>\n",
+ " <th>Deaths per 100k</th>\n",
+ " <th>Positive cases</th>\n",
+ " <th>Positive cases per 100k</th>\n",
+ " </tr>\n",
+ " </thead>\n",
+ " <tbody>\n",
+ " <tr>\n",
+ " <td>Lombardy</td>\n",
+ " <td>13325</td>\n",
+ " <td>132.356672</td>\n",
+ " <td>72889</td>\n",
+ " <td>724.003411</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Emilia-Romagna</td>\n",
+ " <td>3386</td>\n",
+ " <td>75.928186</td>\n",
+ " <td>24450</td>\n",
+ " <td>548.270571</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Piedmont</td>\n",
+ " <td>2823</td>\n",
+ " <td>64.801123</td>\n",
+ " <td>24820</td>\n",
+ " <td>569.735695</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Veneto</td>\n",
+ " <td>1315</td>\n",
+ " <td>26.690655</td>\n",
+ " <td>17471</td>\n",
+ " <td>354.610217</td>\n",
+ " </tr>\n",
+ " <tr>\n",
+ " <td>Liguria</td>\n",
+ " <td>1114</td>\n",
+ " <td>71.841304</td>\n",
+ " <td>7488</td>\n",
+ " <td>482.897384</td>\n",
+ " </tr>\n",
+ " </tbody>\n",
+ "</table>\n",
+ " "
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# get the top 5 U.S. counties\n",
+ "top5_us = get_top5(us_df, key=\"county_state\")\n",
+ "top5_spain = get_top5(spain_df)\n",
+ "top5_italy = get_top5(italy_df)\n",
+ "date = top5_spain.iloc[0].date.strftime(\"%b. %d, %Y\")\n",
+ "\n",
+ "# we will use HTML renderings of these DataFrames to make them look nice on the final notebook\n",
+ "top5_us_html = top5_us[\n",
+ " ['county_state']+columns\n",
+ "].rename(\n",
+ " columns=pretty_print_columns\n",
+ ").to_html(\n",
+ " index=False\n",
+ ")\n",
+ "\n",
+ "top5_spain_html = top5_spain[\n",
+ " ['region_label']+columns\n",
+ "].rename(\n",
+ " columns=pretty_print_columns\n",
+ ").to_html(\n",
+ " index=False\n",
+ ")\n",
+ "\n",
+ "top5_italy_html = top5_italy[\n",
+ " ['region_label']+columns\n",
+ "].rename(\n",
+ " columns=pretty_print_columns\n",
+ ").to_html(\n",
+ " index=False\n",
+ ")\n",
+ "\n",
+ "# display some generic text - we use HTML display for consistency with the rest of the notebook\n",
+ "display(\n",
+ " HTML(\n",
+ " \"\"\"\n",
+ " <h3>\n",
+ " Cummulative deaths attributed to Covid-19 in U.S., Spain and Italy\n",
+ " </h3>\n",
+ " \"\"\"\n",
+ " )\n",
+ ")\n",
+ "\n",
+ "display(\n",
+ " HTML(\n",
+ " f\"\"\"\n",
+ " <h4>United States</h4>\n",
+ " <p style=\"font-size: smaller\">(based on data from {top5_us.iloc[0].date.strftime(\"%b. %d, %Y\")})</p>\n",
+ " {top5_us_html}\n",
+ "\n",
+ " <h4>Spain</h4>\n",
+ " <p style=\"font-size: smaller\">(based on data from {top5_spain.iloc[0].date.strftime(\"%b. %d, %Y\")})</p>\n",
+ " {top5_spain_html}\n",
+ "\n",
+ " <h4>Italy</h4>\n",
+ " <p style=\"font-size: smaller\">(based on data from {top5_italy.iloc[0].date.strftime(\"%b. %d, %Y\")})</p>\n",
+ " {top5_italy_html}\n",
+ " \"\"\"\n",
+ " )\n",
+ ")\n",
+ "\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {
+ "papermill": {
+ "duration": 0.122501,
+ "end_time": "2020-04-28T19:27:58.870650",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:58.748149",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "#\n",
+ "# Here we will create a combined DataFrame for plotting all three datasets at once\n",
+ "#\n",
+ "\n",
+ "# create a common key to use for selecting regions\n",
+ "us_df['plot_key'] = us_df['county_state']\n",
+ "spain_df['plot_key'] = spain_df['region_label']\n",
+ "italy_df['plot_key'] = italy_df['region_label']\n",
+ "\n",
+ "# pull the top-5 region names into a list\n",
+ "top5_regions = top5_us.county_state.to_list() + top5_spain.region_label.to_list() + top5_italy.region_label.to_list()\n",
+ "combined_df = pd.concat([us_df, spain_df, italy_df])"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {
+ "papermill": {
+ "duration": 0.231203,
+ "end_time": "2020-04-28T19:27:59.129182",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:58.897979",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-60c93caba7bf4483a5b9c18f2a0c4c3c\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-60c93caba7bf4483a5b9c18f2a0c4c3c\");\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",
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+ " \"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: ${paths[lib]}`);\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
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+ " function showError(err) {\n",
+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${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",
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+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide\">ECDC</a>, \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, \n",
+ " <a href=\"https://github.com/nytimes/covid-19-data\">The New York Times</a>, \n",
+ " <a href=\"https://github.com/datadista/datasets\">Datadista</a>.\n",
+ "</p>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "<p style=\"font-size: smaller\">Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">\n",
+ " Covid-19 Public Data Collaboration Project @ renkulab.io\n",
+ " </a>\n",
+ " </p>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# generate a simple plots comparing the per-capita cumulative deaths\n",
+ "\n",
+ "base = alt.Chart(combined_df[combined_df.plot_key.isin(top5_regions)])\n",
+ "deaths_100k = plotting.generate_region_chart(\n",
+ " base, \n",
+ " column='deceased_100k', \n",
+ " region_column='plot_key',\n",
+ " ytitle='Deaths per 100k population', \n",
+ " legend_title='Region',\n",
+ " tooltip_title='Deaths/100k'\n",
+ ").properties(\n",
+ " height=350,\n",
+ " width=600,\n",
+ " title='Total deaths per 100k population in the top 5 regions from the U.S., Spain and Italy'\n",
+ ").configure_title(\n",
+ " anchor='start'\n",
+ ")\n",
+ "display(deaths_100k)\n",
+ "display(all_credits)\n",
+ "display(renkulab_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "metadata": {
+ "papermill": {
+ "duration": 0.183614,
+ "end_time": "2020-04-28T19:27:59.335457",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:59.151843",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-be05ed6fb83444aab4da1372aa0b95d3\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-be05ed6fb83444aab4da1372aa0b95d3\");\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: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"start\"}}, \"data\": {\"name\": \"data-c1b22426d34c3ef020c6ca09129afc8d\"}, \"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"plot_key\", \"legend\": {\"title\": \"Region\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector002\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"plot_key\", \"title\": \"Region\"}, {\"type\": \"quantitative\", \"field\": \"deceased\", \"title\": \"Cases\"}, {\"type\": \"temporal\", \"field\": \"date\", \"title\": \"Date\"}], \"x\": {\"type\": \"quantitative\", \"axis\": {\"title\": \"Days since 10th death\"}, \"field\": \"sinceDay0\"}, \"y\": {\"type\": \"quantitative\", \"axis\": {\"title\": \"Cumulative deaths\"}, \"field\": \"deceased\", \"scale\": {\"type\": \"log\"}}}, \"height\": 350, \"selection\": {\"selector002\": {\"type\": \"multi\", \"fields\": [\"plot_key\"], \"bind\": \"legend\"}}, \"title\": \"Top 5 regions from each country: total deaths since 10th death\", \"width\": 600, \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-c1b22426d34c3ef020c6ca09129afc8d\": [{\"index\": 445, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-23T00:00:00\", \"deceased_100k\": 4.217151900984581, \"deceased_daily\": \"\", \"deceased\": 102.0, \"positive_100k\": 84.96320741689523, \"positive_daily\": \"\", \"positive\": 2055, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 0}, {\"index\": 446, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-24T00:00:00\", \"deceased_100k\": 5.126733683549882, \"deceased_daily\": \"\", \"deceased\": 124.0, \"positive_100k\": 101.70778114139284, \"positive_daily\": \"\", \"positive\": 2460, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 1}, {\"index\": 447, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-25T00:00:00\", \"deceased_100k\": 6.821863369239763, \"deceased_daily\": \"\", \"deceased\": 165.0, \"positive_100k\": 121.5532018519085, \"positive_daily\": \"\", \"positive\": 2940, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 2}, {\"index\": 448, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-26T00:00:00\", \"deceased_100k\": 8.516993054929644, \"deceased_daily\": \"\", \"deceased\": 206.0, \"positive_100k\": 144.2100571630806, \"positive_daily\": \"\", \"positive\": 3488, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 3}, {\"index\": 449, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-27T00:00:00\", \"deceased_100k\": 10.418845873020729, \"deceased_daily\": \"\", \"deceased\": 252.0, \"positive_100k\": 170.83599661635577, \"positive_daily\": \"\", \"positive\": 4132, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 4}, {\"index\": 450, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-28T00:00:00\", \"deceased_100k\": 13.271625100157356, \"deceased_daily\": \"\", \"deceased\": 321.0, \"positive_100k\": 198.08210546683455, \"positive_daily\": \"\", \"positive\": 4791, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 5}, {\"index\": 451, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-29T00:00:00\", \"deceased_100k\": 15.710958062491578, \"deceased_daily\": \"\", \"deceased\": 380.0, \"positive_100k\": 223.8398077640247, \"positive_daily\": \"\", \"positive\": 5414, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 6}, {\"index\": 452, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-30T00:00:00\", \"deceased_100k\": 18.274324904266518, \"deceased_daily\": \"\", \"deceased\": 442.0, \"positive_100k\": 239.840178211878, \"positive_daily\": \"\", \"positive\": 5801, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 7}, {\"index\": 453, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-03-31T00:00:00\", \"deceased_100k\": 21.33382726380435, \"deceased_daily\": \"\", \"deceased\": 516.0, \"positive_100k\": 256.7914750687768, \"positive_daily\": \"\", \"positive\": 6211, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 8}, {\"index\": 454, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-01T00:00:00\", \"deceased_100k\": 24.18660649094098, \"deceased_daily\": \"\", \"deceased\": 585.0, \"positive_100k\": 283.08665751021005, \"positive_daily\": \"\", \"positive\": 6847, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 9}, {\"index\": 455, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-02T00:00:00\", \"deceased_100k\": 26.501905573834474, \"deceased_daily\": \"\", \"deceased\": 641.0, \"positive_100k\": 304.0897277621725, \"positive_daily\": \"\", \"positive\": 7355, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 10}, {\"index\": 456, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-03T00:00:00\", \"deceased_100k\": 29.892164945214237, \"deceased_daily\": \"\", \"deceased\": 723.0, \"positive_100k\": 325.5889335318978, \"positive_daily\": \"\", \"positive\": 7875, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 11}, {\"index\": 457, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-04T00:00:00\", \"deceased_100k\": 32.496876413469415, \"deceased_daily\": \"\", \"deceased\": 786.0, \"positive_100k\": 344.48342783336795, \"positive_daily\": \"\", \"positive\": 8332, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 12}, {\"index\": 458, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-05T00:00:00\", \"deceased_100k\": 35.01889862876411, \"deceased_daily\": \"\", \"deceased\": 847.0, \"positive_100k\": 361.72413707562845, \"positive_daily\": \"\", \"positive\": 8749, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 13}, {\"index\": 459, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-06T00:00:00\", \"deceased_100k\": 37.995711735341466, \"deceased_daily\": \"\", \"deceased\": 919.0, \"positive_100k\": 376.89761499387686, \"positive_daily\": \"\", \"positive\": 9116, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 14}, {\"index\": 460, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-07T00:00:00\", \"deceased_100k\": 40.60042320359665, \"deceased_daily\": \"\", \"deceased\": 982.0, \"positive_100k\": 396.1228663071889, \"positive_daily\": \"\", \"positive\": 9581, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 15}, {\"index\": 461, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-08T00:00:00\", \"deceased_100k\": 42.502276021687734, \"deceased_daily\": \"\", \"deceased\": 1028.0, \"positive_100k\": 415.84425313826387, \"positive_daily\": \"\", \"positive\": 10058, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 16}, {\"index\": 462, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-09T00:00:00\", \"deceased_100k\": 44.73488585162075, \"deceased_daily\": \"\", \"deceased\": 1082.0, \"positive_100k\": 434.86278131917476, \"positive_daily\": \"\", \"positive\": 10518, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 17}, {\"index\": 463, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-10T00:00:00\", \"deceased_100k\": 46.67808329619208, \"deceased_daily\": \"\", \"deceased\": 1129.0, \"positive_100k\": 459.0080431836355, \"positive_daily\": \"\", \"positive\": 11102, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 18}, {\"index\": 464, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-11T00:00:00\", \"deceased_100k\": 48.78665924668437, \"deceased_daily\": \"\", \"deceased\": 1180.0, \"positive_100k\": 477.2410234614217, \"positive_daily\": \"\", \"positive\": 11543, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 19}, {\"index\": 465, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-12T00:00:00\", \"deceased_100k\": 50.48178893237424, \"deceased_daily\": \"\", \"deceased\": 1221.0, \"positive_100k\": 501.01418368756026, \"positive_daily\": \"\", \"positive\": 12118, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 20}, {\"index\": 466, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-13T00:00:00\", \"deceased_100k\": 52.218263244544374, \"deceased_daily\": \"\", \"deceased\": 1263.0, \"positive_100k\": 522.0999431924832, \"positive_daily\": \"\", \"positive\": 12628, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 21}, {\"index\": 467, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-14T00:00:00\", \"deceased_100k\": 53.706669797833044, \"deceased_daily\": \"\", \"deceased\": 1299.0, \"positive_100k\": 544.9221770095762, \"positive_daily\": \"\", \"positive\": 13180, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 22}, {\"index\": 468, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-15T00:00:00\", \"deceased_100k\": 55.2777656040822, \"deceased_daily\": \"\", \"deceased\": 1337.0, \"positive_100k\": 566.2973488998608, \"positive_daily\": \"\", \"positive\": 13697, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 23}, {\"index\": 469, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-16T00:00:00\", \"deceased_100k\": 56.724827530890636, \"deceased_daily\": \"\", \"deceased\": 1372.0, \"positive_100k\": 594.5357287858654, \"positive_daily\": \"\", \"positive\": 14380, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 24}, {\"index\": 470, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-17T00:00:00\", \"deceased_100k\": 57.923821698817626, \"deceased_daily\": \"\", \"deceased\": 1401.0, \"positive_100k\": 616.1589684350315, \"positive_daily\": \"\", \"positive\": 14903, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 25}, {\"index\": 471, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-18T00:00:00\", \"deceased_100k\": 59.08147124026438, \"deceased_daily\": \"\", \"deceased\": 1429.0, \"positive_100k\": 632.2833727623254, \"positive_daily\": \"\", \"positive\": 15293, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 26}, {\"index\": 472, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-19T00:00:00\", \"deceased_100k\": 60.28046540819136, \"deceased_daily\": \"\", \"deceased\": 1458.0, \"positive_100k\": 645.8444102478445, \"positive_daily\": \"\", \"positive\": 15621, \"region_iso\": \"ES-CL\", \"region_label\": \"Castilla y Le\\u00f3n\", \"tested_100k\": \"\", \"tested\": \"\", \"county_state\": null, \"plot_key\": \"Castilla y Le\\u00f3n\", \"sinceDay0\": 27}, {\"index\": 473, \"admin2_label\": \"\", \"admin2\": \"\", \"country_label\": \"Spain\", \"country\": \"ESP\", \"date\": \"2020-04-20T00:00:00\", \"deceased_100k\": 61.72752733499979, \"deceased_daily\": \"\", \"deceased\": 1493.0, 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\"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 5}, {\"index\": 7866, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-06T00:00:00\", \"deceased_100k\": 19.778854118374728, \"deceased_daily\": \"\", \"deceased\": 346.0, \"positive_100k\": 472.74891202011275, \"positive_daily\": \"\", \"positive\": 8270, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 6}, {\"index\": 7867, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-07T00:00:00\", \"deceased_100k\": 22.98005594100185, \"deceased_daily\": \"\", \"deceased\": 402.0, \"positive_100k\": 517.0512586725416, \"positive_daily\": \"\", \"positive\": 9045, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 7}, {\"index\": 7868, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-08T00:00:00\", \"deceased_100k\": 25.49528594449459, \"deceased_daily\": \"\", \"deceased\": 446.0, \"positive_100k\": 550.263727582298, \"positive_daily\": \"\", \"positive\": 9626, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 8}, {\"index\": 7869, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-09T00:00:00\", \"deceased_100k\": 28.810816403644107, \"deceased_daily\": \"\", \"deceased\": 504.0, \"positive_100k\": 576.9594642102778, \"positive_daily\": \"\", \"positive\": 10093, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 9}, {\"index\": 7870, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-10T00:00:00\", \"deceased_100k\": 34.813069821069966, \"deceased_daily\": \"\", \"deceased\": 609.0, \"positive_100k\": 602.4547501547725, \"positive_daily\": \"\", \"positive\": 10539, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 10}, {\"index\": 7871, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-11T00:00:00\", \"deceased_100k\": 37.27113550630151, \"deceased_daily\": \"\", \"deceased\": 652.0, \"positive_100k\": 626.0064492783862, \"positive_daily\": \"\", \"positive\": 10951, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 11}, {\"index\": 7872, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-12T00:00:00\", \"deceased_100k\": 40.24368005588384, \"deceased_daily\": \"\", \"deceased\": 704.0, \"positive_100k\": 638.1824490680216, \"positive_daily\": \"\", \"positive\": 11164, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 12}, {\"index\": 7873, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-13T00:00:00\", \"deceased_100k\": 43.44488187851096, \"deceased_daily\": \"\", \"deceased\": 760.0, \"positive_100k\": 665.8499791064418, \"positive_daily\": \"\", \"positive\": 11648, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 13}, {\"index\": 7874, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-14T00:00:00\", \"deceased_100k\": 46.87474097418288, \"deceased_daily\": \"\", \"deceased\": 820.0, \"positive_100k\": 697.919161650974, \"positive_daily\": \"\", \"positive\": 12209, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 14}, {\"index\": 7875, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-15T00:00:00\", \"deceased_100k\": 50.533257342899596, \"deceased_daily\": \"\", \"deceased\": 884.0, \"positive_100k\": 717.0692082684757, \"positive_daily\": \"\", \"positive\": 12544, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 15}, {\"index\": 7876, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-16T00:00:00\", \"deceased_100k\": 56.07819621423586, \"deceased_daily\": \"\", \"deceased\": 981.0, \"positive_100k\": 743.2504660321047, \"positive_daily\": \"\", \"positive\": 13002, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 16}, {\"index\": 7877, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-17T00:00:00\", \"deceased_100k\": 59.67954826469138, \"deceased_daily\": \"\", \"deceased\": 1044.0, \"positive_100k\": 756.4554235504415, \"positive_daily\": \"\", \"positive\": 13233, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 17}, {\"index\": 7878, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-18T00:00:00\", \"deceased_100k\": 61.16582053948253, \"deceased_daily\": \"\", \"deceased\": 1070.0, \"positive_100k\": 770.0605312966068, \"positive_daily\": \"\", \"positive\": 13471, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 18}, {\"index\": 7879, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-19T00:00:00\", \"deceased_100k\": 63.96687213428127, \"deceased_daily\": \"\", \"deceased\": 1119.0, \"positive_100k\": 782.6938456323317, \"positive_daily\": \"\", \"positive\": 13692, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 19}, {\"index\": 7880, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-20T00:00:00\", \"deceased_100k\": 65.62463736385602, \"deceased_daily\": \"\", \"deceased\": 1148.0, \"positive_100k\": 795.2699956497954, \"positive_daily\": \"\", \"positive\": 13912, 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832.3696382013134, \"positive_daily\": \"\", \"positive\": 14561, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 22}, {\"index\": 7883, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-23T00:00:00\", \"deceased_100k\": 79.80138829263329, \"deceased_daily\": \"\", \"deceased\": 1396.0, \"positive_100k\": 857.1217880084123, \"positive_daily\": \"\", \"positive\": 14994, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 23}, {\"index\": 7884, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-24T00:00:00\", \"deceased_100k\": 82.48811125090963, \"deceased_daily\": \"\", \"deceased\": 1443.0, \"positive_100k\": 880.7306514502874, \"positive_daily\": \"\", \"positive\": 15407, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 24}, {\"index\": 7885, \"admin2_label\": \"Wayne\", \"admin2\": \"\", \"country_label\": \"United States of America\", \"country\": \"USA\", \"date\": \"2020-04-25T00:00:00\", \"deceased_100k\": 89.17633648746987, \"deceased_daily\": \"\", \"deceased\": 1560.0, \"positive_100k\": 888.7908203251164, \"positive_daily\": \"\", \"positive\": 15548, \"region_iso\": \"\", \"region_label\": \"Michigan\", \"tested_100k\": null, \"tested\": null, \"county_state\": \"Wayne, Michigan\", \"plot_key\": \"Wayne, Michigan\", \"sinceDay0\": 25}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.Chart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://www.ecdc.europa.eu/en/publications-data/download-todays-data-geographic-distribution-covid-19-cases-worldwide\">ECDC</a>, \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, \n",
+ " <a href=\"https://github.com/nytimes/covid-19-data\">The New York Times</a>, \n",
+ " <a href=\"https://github.com/datadista/datasets\">Datadista</a>.\n",
+ "</p>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "<p style=\"font-size: smaller\">Analysis and Visualization:\n",
+ " <a href=\"https://renkulab.io/projects/covid-19/covid-19-public-data\">\n",
+ " Covid-19 Public Data Collaboration Project @ renkulab.io\n",
+ " </a>\n",
+ " </p>\n"
+ ],
+ "text/plain": [
+ "<IPython.core.display.HTML object>"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ }
+ ],
+ "source": [
+ "# Now for a slightly more complicated plot, we make use of some of the helper functions\n",
+ "\n",
+ "# Making a plot of the evolution of the death count since the 10th death in each region\n",
+ "since_10th_death = helper.make_since_df(\n",
+ " combined_df[combined_df.plot_key.isin(top5_regions)], \n",
+ " 'deceased', \n",
+ " 'plot_key'\n",
+ ")\n",
+ "\n",
+ "base = alt.Chart(\n",
+ " since_10th_death, \n",
+ " title=\"Top 5 regions from each country: total deaths since 10th death\"\n",
+ ").encode(\n",
+ " alt.Y(scale=alt.Scale(type='log'))\n",
+ ")\n",
+ "\n",
+ "line_chart = plotting.make_region_since_chart(\n",
+ " base, \n",
+ " 'deceased', \n",
+ " 'sinceDay0', \n",
+ " 'plot_key', \n",
+ " 'Days since 10th death',\n",
+ " 'Cumulative deaths',\n",
+ " 'Cases',\n",
+ " 'Region'\n",
+ ").properties(\n",
+ " width=600,\n",
+ " height=350\n",
+ ").configure_title(\n",
+ " anchor='start'\n",
+ ")\n",
+ "display(line_chart)\n",
+ "display(all_credits)\n",
+ "display(renkulab_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "metadata": {
+ "papermill": {
+ "duration": 0.067679,
+ "end_time": "2020-04-28T19:27:59.434948",
+ "exception": false,
+ "start_time": "2020-04-28T19:27:59.367269",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/plain": [
+ "[]"
+ ]
+ },
+ "execution_count": 19,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "[]"
+ ]
+ }
+ ],
+ "metadata": {
+ "file_extension": ".py",
+ "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"
+ },
+ "mimetype": "text/x-python",
+ "name": "python",
+ "npconvert_exporter": "python",
+ "papermill": {
+ "duration": 6.934144,
+ "end_time": "2020-04-28T19:27:59.784501",
+ "environment_variables": {},
+ "exception": null,
+ "input_path": "notebooks/datasets_summary.ipynb",
+ "output_path": "runs/dataset_summary.run.ipynb",
+ "parameters": {
+ "atlas_path": "data/atlas/",
+ "data_path": "data/"
+ },
+ "start_time": "2020-04-28T19:27:52.850357",
+ "version": "1.1.0"
+ },
+ "pygments_lexer": "ipython3",
+ "version": 3
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
\ No newline at end of file
--
GitLab