From 5c7cf6a1681ee253a92f1da90cdc295d34f0165c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Rok=20Ro=C5=A1kar?= <rok.roskar@sdsc.ethz.ch>
Date: Fri, 10 Apr 2020 10:55:07 +0000
Subject: [PATCH] renku run papermill notebooks/covid-19-italy.ipynb
runs/covid-19-italy.run.ipynb -p data_folder ./data/covid-19-italy/
---
...66aed5154987aa505ac946f1e25a_papermill.cwl | 67 ++
runs/covid-19-italy.run.ipynb | 1045 +++++++++++++++++
2 files changed, 1112 insertions(+)
create mode 100644 .renku/workflow/4a3366aed5154987aa505ac946f1e25a_papermill.cwl
create mode 100644 runs/covid-19-italy.run.ipynb
diff --git a/.renku/workflow/4a3366aed5154987aa505ac946f1e25a_papermill.cwl b/.renku/workflow/4a3366aed5154987aa505ac946f1e25a_papermill.cwl
new file mode 100644
index 000000000..f69bd8064
--- /dev/null
+++ b/.renku/workflow/4a3366aed5154987aa505ac946f1e25a_papermill.cwl
@@ -0,0 +1,67 @@
+arguments: []
+baseCommand:
+- papermill
+class: CommandLineTool
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default:
+ class: File
+ path: ../../notebooks/covid-19-italy.ipynb
+ inputBinding:
+ position: 1
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: File
+ input_2:
+ default: runs/covid-19-italy.run.ipynb
+ inputBinding:
+ position: 2
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_3:
+ default: data_folder
+ inputBinding:
+ position: 3
+ prefix: -p
+ separate: true
+ shellQuote: true
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: Directory
+ listing: []
+ path: ../../data/covid-19-italy
+ inputBinding:
+ position: 4
+ separate: true
+ shellQuote: true
+ 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/covid-19-italy.ipynb
+ writable: false
+ - entry: $(inputs.input_4)
+ entryname: data/covid-19-italy
+ writable: false
+successCodes: []
+temporaryFailCodes: []
diff --git a/runs/covid-19-italy.run.ipynb b/runs/covid-19-italy.run.ipynb
new file mode 100644
index 000000000..5dc17b28d
--- /dev/null
+++ b/runs/covid-19-italy.run.ipynb
@@ -0,0 +1,1045 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.030107,
+ "end_time": "2020-04-10T10:55:02.082530",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:02.052423",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "# COVID-19 Case data for Italy\n",
+ "\n",
+ "Data from [Civil Protection of Italy](https://github.com/pcm-dpc/COVID-19).\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 1,
+ "metadata": {
+ "papermill": {
+ "duration": 0.056103,
+ "end_time": "2020-04-10T10:55:02.152323",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:02.096220",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "%load_ext autoreload\n",
+ "%autoreload 2"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 2,
+ "metadata": {
+ "papermill": {
+ "duration": 0.52297,
+ "end_time": "2020-04-10T10:55:02.697416",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:02.174446",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "import pandas as pd\n",
+ "import altair as alt\n",
+ "\n",
+ "from IPython.display import display, HTML\n",
+ "\n",
+ "from covid_19_utils import helper, plotting\n",
+ "from covid_19_utils.italy_utils import get_region_populations, prepare_dataframe"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "metadata": {
+ "papermill": {
+ "duration": 0.054624,
+ "end_time": "2020-04-10T10:55:02.778044",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:02.723420",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "html_credits=HTML('''\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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": 4,
+ "metadata": {
+ "papermill": {
+ "duration": 0.055666,
+ "end_time": "2020-04-10T10:55:02.849037",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:02.793371",
+ "status": "completed"
+ },
+ "tags": [
+ "parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "data_folder = \"../../data/covid-19-italy/\""
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "metadata": {
+ "papermill": {
+ "duration": 0.044733,
+ "end_time": "2020-04-10T10:55:02.917693",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:02.872960",
+ "status": "completed"
+ },
+ "tags": [
+ "injected-parameters"
+ ]
+ },
+ "outputs": [],
+ "source": [
+ "# Parameters\n",
+ "data_folder = \"./data/covid-19-italy/\"\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "metadata": {
+ "papermill": {
+ "duration": 0.069435,
+ "end_time": "2020-04-10T10:55:03.010582",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:02.941147",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "df_national = prepare_dataframe(\n",
+ " data_folder, \n",
+ " \"dpc-covid19-ita-andamento-nazionale.csv\", \n",
+ " \"dati-andamento-nazionale-description.json\",\n",
+ " use_time_index=True\n",
+ ")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "metadata": {
+ "papermill": {
+ "duration": 0.061512,
+ "end_time": "2020-04-10T10:55:03.098284",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:03.036772",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# compute daily new cases\n",
+ "df_national.reset_index(level=0, inplace=True)\n",
+ "df_national[\"New cases per day\"] = df_national[\"total_cases\"].diff()"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.014033,
+ "end_time": "2020-04-10T10:55:03.132415",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:03.118382",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## National summary of total cases and tests"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 8,
+ "metadata": {
+ "papermill": {
+ "duration": 0.105589,
+ "end_time": "2020-04-10T10:55:03.251446",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:03.145857",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-af3ba437940245809b635d2fa9ceb7c9\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-af3ba437940245809b635d2fa9ceb7c9\");\n",
+ " const paths = {\n",
+ " \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
+ " \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
+ " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
+ " };\n",
+ "\n",
+ " function loadScript(lib) {\n",
+ " return new Promise(function(resolve, reject) {\n",
+ " var s = document.createElement('script');\n",
+ " s.src = paths[lib];\n",
+ " s.async = true;\n",
+ " s.onload = () => resolve(paths[lib]);\n",
+ " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
+ " });\n",
+ " }\n",
+ "\n",
+ " function showError(err) {\n",
+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
+ " throw err;\n",
+ " }\n",
+ "\n",
+ " function displayChart(vegaEmbed) {\n",
+ " vegaEmbed(outputDiv, spec, embedOpt)\n",
+ " .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
+ " }\n",
+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"hconcat\": [{\"layer\": [{\"mark\": {\"type\": \"bar\", \"size\": 10}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"tests\", \"title\": \"Tests (blue)\"}}}, {\"mark\": {\"type\": \"point\", \"color\": \"orange\", \"filled\": true, \"opacity\": 1, \"size\": 100}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases\", \"title\": \"Cases (orange)\"}}}]}, {\"mark\": {\"type\": \"bar\", \"size\": 10}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"New cases per day\"}}}], \"data\": {\"name\": \"data-8105e5bad8e6a91345bf5e14e2e7058d\"}, \"title\": \"Total and daily tests and cases nationwide\", \"$schema\": 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3557, \"intensive_care\": 650, \"total_hospitalised\": 4207, \"home_confinement\": 2180, \"total_positive\": 6387, \"new_current_positive\": 1326, \"new_positive\": 1492, \"recovered\": 622, \"dead\": 366, \"total_cases\": 7375, \"tests\": 49937, \"New cases per day\": 1492.0}, {\"date\": \"2020-03-09T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 4316, \"intensive_care\": 733, \"total_hospitalised\": 5049, \"home_confinement\": 2936, \"total_positive\": 7985, \"new_current_positive\": 1598, \"new_positive\": 1797, \"recovered\": 724, \"dead\": 463, \"total_cases\": 9172, \"tests\": 53826, \"New cases per day\": 1797.0}, {\"date\": \"2020-03-10T18:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 5038, \"intensive_care\": 877, \"total_hospitalised\": 5915, \"home_confinement\": 2599, \"total_positive\": 8514, \"new_current_positive\": 529, \"new_positive\": 977, \"recovered\": 1004, \"dead\": 631, \"total_cases\": 10149, \"tests\": 60761, \"New cases per day\": 977.0}, {\"date\": \"2020-03-11T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 5838, \"intensive_care\": 1028, \"total_hospitalised\": 6866, \"home_confinement\": 3724, \"total_positive\": 10590, \"new_current_positive\": 2076, \"new_positive\": 2313, \"recovered\": 1045, \"dead\": 827, \"total_cases\": 12462, \"tests\": 73154, \"New cases per day\": 2313.0}, {\"date\": \"2020-03-12T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 6650, \"intensive_care\": 1153, \"total_hospitalised\": 7803, \"home_confinement\": 5036, \"total_positive\": 12839, \"new_current_positive\": 2249, \"new_positive\": 2651, \"recovered\": 1258, \"dead\": 1016, \"total_cases\": 15113, \"tests\": 86011, \"New cases per day\": 2651.0}, {\"date\": \"2020-03-13T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 7426, \"intensive_care\": 1328, \"total_hospitalised\": 8754, \"home_confinement\": 6201, \"total_positive\": 14955, \"new_current_positive\": 2116, \"new_positive\": 2547, \"recovered\": 1439, \"dead\": 1266, \"total_cases\": 17660, \"tests\": 97488, \"New cases per day\": 2547.0}, {\"date\": \"2020-03-14T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 8372, \"intensive_care\": 1518, \"total_hospitalised\": 9890, \"home_confinement\": 7860, \"total_positive\": 17750, \"new_current_positive\": 2795, \"new_positive\": 3497, \"recovered\": 1966, \"dead\": 1441, \"total_cases\": 21157, \"tests\": 109170, \"New cases per day\": 3497.0}, {\"date\": \"2020-03-15T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 9663, \"intensive_care\": 1672, \"total_hospitalised\": 11335, \"home_confinement\": 9268, \"total_positive\": 20603, \"new_current_positive\": 2853, \"new_positive\": 3590, \"recovered\": 2335, \"dead\": 1809, \"total_cases\": 24747, \"tests\": 124899, \"New cases per day\": 3590.0}, {\"date\": \"2020-03-16T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 11025, \"intensive_care\": 1851, \"total_hospitalised\": 12876, \"home_confinement\": 10197, \"total_positive\": 23073, \"new_current_positive\": 2470, \"new_positive\": 3233, \"recovered\": 2749, \"dead\": 2158, \"total_cases\": 27980, \"tests\": 137962, \"New cases per day\": 3233.0}, {\"date\": \"2020-03-17T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 12894, \"intensive_care\": 2060, \"total_hospitalised\": 14954, \"home_confinement\": 11108, \"total_positive\": 26062, \"new_current_positive\": 2989, \"new_positive\": 3526, \"recovered\": 2941, \"dead\": 2503, \"total_cases\": 31506, \"tests\": 148657, \"New cases per day\": 3526.0}, {\"date\": \"2020-03-18T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 14363, \"intensive_care\": 2257, \"total_hospitalised\": 16620, \"home_confinement\": 12090, \"total_positive\": 28710, \"new_current_positive\": 2648, \"new_positive\": 4207, \"recovered\": 4025, \"dead\": 2978, \"total_cases\": 35713, \"tests\": 165541, \"New cases per day\": 4207.0}, {\"date\": \"2020-03-19T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 15757, \"intensive_care\": 2498, \"total_hospitalised\": 18255, \"home_confinement\": 14935, \"total_positive\": 33190, \"new_current_positive\": 4480, \"new_positive\": 5322, \"recovered\": 4440, \"dead\": 3405, \"total_cases\": 41035, \"tests\": 182777, \"New cases per day\": 5322.0}, {\"date\": \"2020-03-20T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 16020, \"intensive_care\": 2655, \"total_hospitalised\": 18675, \"home_confinement\": 19185, \"total_positive\": 37860, \"new_current_positive\": 4670, \"new_positive\": 5986, \"recovered\": 5129, \"dead\": 4032, \"total_cases\": 47021, \"tests\": 206886, \"New cases per day\": 5986.0}, {\"date\": \"2020-03-21T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 17708, \"intensive_care\": 2857, \"total_hospitalised\": 20565, \"home_confinement\": 22116, \"total_positive\": 42681, \"new_current_positive\": 4821, \"new_positive\": 6557, \"recovered\": 6072, \"dead\": 4825, \"total_cases\": 53578, \"tests\": 233222, \"New cases per day\": 6557.0}, {\"date\": \"2020-03-22T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 19846, \"intensive_care\": 3009, \"total_hospitalised\": 22855, \"home_confinement\": 23783, \"total_positive\": 46638, \"new_current_positive\": 3957, \"new_positive\": 5560, \"recovered\": 7024, \"dead\": 5476, \"total_cases\": 59138, \"tests\": 258402, \"New cases per day\": 5560.0}, {\"date\": \"2020-03-23T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 20692, \"intensive_care\": 3204, \"total_hospitalised\": 23896, \"home_confinement\": 26522, \"total_positive\": 50418, \"new_current_positive\": 3780, \"new_positive\": 4789, \"recovered\": 7432, \"dead\": 6077, \"total_cases\": 63927, \"tests\": 275468, \"New cases per day\": 4789.0}, {\"date\": \"2020-03-24T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 21937, \"intensive_care\": 3396, \"total_hospitalised\": 25333, \"home_confinement\": 28697, \"total_positive\": 54030, \"new_current_positive\": 3612, \"new_positive\": 5249, \"recovered\": 8326, \"dead\": 6820, \"total_cases\": 69176, \"tests\": 296964, \"New cases per day\": 5249.0}, {\"date\": \"2020-03-25T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 23112, \"intensive_care\": 3489, \"total_hospitalised\": 26601, \"home_confinement\": 30920, \"total_positive\": 57521, \"new_current_positive\": 3491, \"new_positive\": 5210, \"recovered\": 9362, \"dead\": 7503, \"total_cases\": 74386, \"tests\": 324445, \"New cases per day\": 5210.0}, {\"date\": \"2020-03-26T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 24753, \"intensive_care\": 3612, \"total_hospitalised\": 28365, \"home_confinement\": 33648, \"total_positive\": 62013, \"new_current_positive\": 4492, \"new_positive\": 6153, \"recovered\": 10361, \"dead\": 8165, \"total_cases\": 80539, \"tests\": 361060, \"New cases per day\": 6153.0}, {\"date\": \"2020-03-27T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 26029, \"intensive_care\": 3732, \"total_hospitalised\": 29761, \"home_confinement\": 36653, \"total_positive\": 66414, \"new_current_positive\": 4401, \"new_positive\": 5959, \"recovered\": 10950, \"dead\": 9134, \"total_cases\": 86498, \"tests\": 394079, \"New cases per day\": 5959.0}, {\"date\": \"2020-03-28T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 26676, \"intensive_care\": 3856, \"total_hospitalised\": 30532, \"home_confinement\": 39533, \"total_positive\": 70065, \"new_current_positive\": 3651, \"new_positive\": 5974, \"recovered\": 12384, \"dead\": 10023, \"total_cases\": 92472, \"tests\": 429526, \"New cases per day\": 5974.0}, {\"date\": \"2020-03-29T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 27386, \"intensive_care\": 3906, \"total_hospitalised\": 31292, \"home_confinement\": 42588, \"total_positive\": 73880, \"new_current_positive\": 3815, \"new_positive\": 5217, \"recovered\": 13030, \"dead\": 10779, \"total_cases\": 97689, \"tests\": 454030, \"New cases per day\": 5217.0}, {\"date\": \"2020-03-30T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 27795, \"intensive_care\": 3981, \"total_hospitalised\": 31776, \"home_confinement\": 43752, \"total_positive\": 75528, \"new_current_positive\": 1648, \"new_positive\": 4050, \"recovered\": 14620, \"dead\": 11591, \"total_cases\": 101739, \"tests\": 477359, \"New cases per day\": 4050.0}, {\"date\": \"2020-03-31T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28192, \"intensive_care\": 4023, \"total_hospitalised\": 32215, \"home_confinement\": 45420, \"total_positive\": 77635, \"new_current_positive\": 2107, \"new_positive\": 4053, \"recovered\": 15729, \"dead\": 12428, \"total_cases\": 105792, \"tests\": 506968, \"New cases per day\": 4053.0}, {\"date\": \"2020-04-01T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28403, \"intensive_care\": 4035, \"total_hospitalised\": 32438, \"home_confinement\": 48134, \"total_positive\": 80572, \"new_current_positive\": 2937, \"new_positive\": 4782, \"recovered\": 16847, \"dead\": 13155, \"total_cases\": 110574, \"tests\": 541423, \"New cases per day\": 4782.0}, {\"date\": \"2020-04-02T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28540, \"intensive_care\": 4053, \"total_hospitalised\": 32593, \"home_confinement\": 50456, \"total_positive\": 83049, \"new_current_positive\": 2477, \"new_positive\": 4668, \"recovered\": 18278, \"dead\": 13915, \"total_cases\": 115242, \"tests\": 581232, \"New cases per day\": 4668.0}, {\"date\": \"2020-04-03T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28741, \"intensive_care\": 4068, \"total_hospitalised\": 32809, \"home_confinement\": 52579, \"total_positive\": 85388, \"new_current_positive\": 2339, \"new_positive\": 4585, \"recovered\": 19758, \"dead\": 14681, \"total_cases\": 119827, \"tests\": 619849, \"New cases per day\": 4585.0}, {\"date\": \"2020-04-04T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 29010, \"intensive_care\": 3994, \"total_hospitalised\": 33004, \"home_confinement\": 55270, \"total_positive\": 88274, \"new_current_positive\": 2886, \"new_positive\": 4805, \"recovered\": 20996, \"dead\": 15362, \"total_cases\": 124632, \"tests\": 657224, \"New cases per day\": 4805.0}, {\"date\": \"2020-04-05T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28949, \"intensive_care\": 3977, \"total_hospitalised\": 32926, \"home_confinement\": 58320, \"total_positive\": 91246, \"new_current_positive\": 2972, \"new_positive\": 4316, \"recovered\": 21815, \"dead\": 15887, \"total_cases\": 128948, \"tests\": 691461, \"New cases per day\": 4316.0}, {\"date\": \"2020-04-06T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28976, \"intensive_care\": 3898, \"total_hospitalised\": 32874, \"home_confinement\": 60313, \"total_positive\": 93187, \"new_current_positive\": 1941, \"new_positive\": 3599, \"recovered\": 22837, \"dead\": 16523, \"total_cases\": 132547, \"tests\": 721732, \"New cases per day\": 3599.0}, {\"date\": \"2020-04-07T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28718, \"intensive_care\": 3792, \"total_hospitalised\": 32510, \"home_confinement\": 61557, \"total_positive\": 94067, \"new_current_positive\": 880, \"new_positive\": 3039, \"recovered\": 24392, \"dead\": 17127, \"total_cases\": 135586, \"tests\": 755445, \"New cases per day\": 3039.0}, {\"date\": \"2020-04-08T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28485, \"intensive_care\": 3693, \"total_hospitalised\": 32178, \"home_confinement\": 63084, \"total_positive\": 95262, \"new_current_positive\": 1195, \"new_positive\": 3836, \"recovered\": 26491, \"dead\": 17669, \"total_cases\": 139422, \"tests\": 807125, \"New cases per day\": 3836.0}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.HConcatChart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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": [
+ "# make the charts\n",
+ "base = alt.Chart(df_national).mark_bar(size=10).encode(alt.X('date'))\n",
+ "daily = base.encode(alt.Y('New cases per day'))\n",
+ "total = base.mark_point(color='orange', filled=True, size=100, opacity=1).encode(alt.Y('total_cases', title=\"Cases (orange)\"))\n",
+ "tests = base.encode(alt.Y('tests', title=\"Tests (blue)\"))\n",
+ "totals = alt.layer(tests, total)\n",
+ "chart = alt.hconcat(totals, daily, \n",
+ " title='Total and daily tests and cases nationwide'\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "metadata": {
+ "papermill": {
+ "duration": 0.079957,
+ "end_time": "2020-04-10T10:55:03.352798",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:03.272841",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# set up the regional data frame\n",
+ "df_regions = prepare_dataframe(\n",
+ " data_folder, \n",
+ " \"dpc-covid19-ita-regioni.csv\", \n",
+ " \"dati-regioni-description.json\",\n",
+ " use_time_index=True\n",
+ ")\n",
+ "df_regions.reset_index(level=0, inplace=True)\n",
+ "\n",
+ "# The regional data includes Bolzano and Trento as separate regions - they are two provinces of the Trentino Alto Adige region, so merge them together\n",
+ "df_trentino_alto_adige = df_regions.loc[df_regions['region_code'] == 4].groupby('date').sum().reset_index()\n",
+ "df_trentino_alto_adige['region_code'] = 4\n",
+ "df_trentino_alto_adige['latitude'] = 46.4337\n",
+ "df_trentino_alto_adige['longitude'] = 11.1693\n",
+ "df_trentino_alto_adige['region'] = 'Trentino Alto Adige'\n",
+ "df_trentino_alto_adige['country_code'] = 'ITA' \n",
+ "df_regions = df_regions[df_regions['region_code'] !=4 ].append(df_trentino_alto_adige)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "metadata": {
+ "papermill": {
+ "duration": 1.030607,
+ "end_time": "2020-04-10T10:55:04.406071",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:03.375464",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# Retrieve population data and include it in the dataframe\n",
+ "\n",
+ "\n",
+ "\n",
+ "populations = get_region_populations()\n",
+ "\n",
+ "for field in ['total_cases', 'tests', 'dead']:\n",
+ " df_regions[f'{field}_100k'] = df_regions[[field,'region_code']].apply(lambda row: row[field]/populations[row['region_code']]*100000, axis=1)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "metadata": {
+ "papermill": {
+ "duration": 0.06809,
+ "end_time": "2020-04-10T10:55:04.504335",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:04.436245",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "max_cases = df_regions.set_index('region').max(level='region')['total_cases'].reset_index()\n",
+ "\n",
+ "sorted_regions = max_cases.sort_values(by='total_cases', ascending=False)['region']"
+ ]
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.013373,
+ "end_time": "2020-04-10T10:55:04.542520",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:04.529147",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## Cases per region"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "metadata": {
+ "papermill": {
+ "duration": 0.193005,
+ "end_time": "2020-04-10T10:55:04.756300",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:04.563295",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-488db66d90704327803affde53bc8735\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-488db66d90704327803affde53bc8735\");\n",
+ " const paths = {\n",
+ " \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
+ " \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
+ " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
+ " };\n",
+ "\n",
+ " function loadScript(lib) {\n",
+ " return new Promise(function(resolve, reject) {\n",
+ " var s = document.createElement('script');\n",
+ " s.src = paths[lib];\n",
+ " s.async = true;\n",
+ " s.onload = () => resolve(paths[lib]);\n",
+ " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
+ " });\n",
+ " }\n",
+ "\n",
+ " function showError(err) {\n",
+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
+ " throw err;\n",
+ " }\n",
+ "\n",
+ " function displayChart(vegaEmbed) {\n",
+ " vegaEmbed(outputDiv, spec, embedOpt)\n",
+ " .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
+ " }\n",
+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"data\": {\"name\": \"data-1302be15f303e6683aab8d2ebee99814\"}, \"facet\": {\"type\": \"nominal\", \"field\": \"region\"}, \"spec\": {\"layer\": [{\"mark\": {\"type\": \"bar\", \"color\": \"orange\", \"size\": 5}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases\", \"title\": \"Total cases\"}}, \"height\": 150, \"width\": 150}, {\"mark\": {\"type\": \"line\", \"color\": \"black\"}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"dead\", \"title\": \"Deaths\"}}}]}, \"align\": \"each\", \"columns\": 5, \"title\": \"Total cases (orange) and deaths (black) by region\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-1302be15f303e6683aab8d2ebee99814\": [{\"date\": 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\"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 18, \"region\": \"Calabria\", \"latitude\": 38.90597598, \"longitude\": 16.59440194, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 1, \"total_cases_100k\": 0.0, \"tests_100k\": 0.05135761281598413, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 15, \"region\": \"Campania\", \"latitude\": 40.83956555, \"longitude\": 14.25084984, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 10, \"total_cases_100k\": 0.0, \"tests_100k\": 0.17035876704545938, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 8, \"region\": \"Emilia-Romagna\", \"latitude\": 44.49436681, \"longitude\": 11.341720800000001, \"hospitalised_with_symptoms\": 10, \"intensive_care\": 2, \"total_hospitalised\": 12, \"home_confinement\": 6, \"total_positive\": 18, \"new_current_positive\": 0, \"new_positive\": 18, \"recovered\": 0, \"dead\": 0, \"total_cases\": 18, \"tests\": 148, \"total_cases_100k\": 0.4036347760062447, \"tests_100k\": 3.318774824940234, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 6, \"region\": \"Friuli Venezia Giulia\", \"latitude\": 45.6494354, \"longitude\": 13.76813649, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 58, \"total_cases_100k\": 0.0, \"tests_100k\": 4.7727983410411285, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 12, \"region\": \"Lazio\", \"latitude\": 41.89277044, \"longitude\": 12.48366722, \"hospitalised_with_symptoms\": 1, \"intensive_care\": 1, \"total_hospitalised\": 2, \"home_confinement\": 0, \"total_positive\": 2, \"new_current_positive\": 0, \"new_positive\": 2, \"recovered\": 1, \"dead\": 0, \"total_cases\": 3, \"tests\": 124, \"total_cases_100k\": 0.051028374838112484, \"tests_100k\": 2.1091728266419825, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 7, \"region\": \"Liguria\", \"latitude\": 44.41149315, \"longitude\": 8.9326992, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 1, \"total_cases_100k\": 0.0, 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\"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 584, \"intensive_care\": 140, \"total_hospitalised\": 724, \"home_confinement\": 1731, \"total_positive\": 2455, \"new_current_positive\": 128, \"new_positive\": 199, \"recovered\": 331, \"dead\": 221, \"total_cases\": 3007, \"tests\": 17017, \"total_cases_100k\": 280.4315306879945, \"tests_100k\": 1586.998123617427, \"dead_100k\": 20.610365241784766}, {\"date\": \"2020-03-31T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 603, \"intensive_care\": 142, \"total_hospitalised\": 745, \"home_confinement\": 1786, \"total_positive\": 2531, \"new_current_positive\": 76, \"new_positive\": 110, \"recovered\": 346, \"dead\": 240, \"total_cases\": 3117, \"tests\": 18248, \"total_cases_100k\": 290.690083523272, \"tests_100k\": 1701.8006558013049, \"dead_100k\": 22.382297095150875}, {\"date\": \"2020-04-01T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 614, \"intensive_care\": 133, \"total_hospitalised\": 747, \"home_confinement\": 1848, \"total_positive\": 2595, \"new_current_positive\": 64, \"new_positive\": 171, \"recovered\": 404, \"dead\": 289, \"total_cases\": 3288, \"tests\": 19626, \"total_cases_100k\": 306.637470203567, \"tests_100k\": 1830.3123449559628, \"dead_100k\": 26.952016085410843}, {\"date\": \"2020-04-02T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 618, \"intensive_care\": 138, \"total_hospitalised\": 756, \"home_confinement\": 1991, \"total_positive\": 2747, \"new_current_positive\": 152, \"new_positive\": 194, \"recovered\": 419, \"dead\": 316, \"total_cases\": 3482, \"tests\": 21173, \"total_cases_100k\": 324.7298270221473, \"tests_100k\": 1974.5849016484563, \"dead_100k\": 29.47002450861532}, {\"date\": \"2020-04-03T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 634, \"intensive_care\": 140, \"total_hospitalised\": 774, \"home_confinement\": 2094, \"total_positive\": 2868, \"new_current_positive\": 121, \"new_positive\": 186, \"recovered\": 457, \"dead\": 343, \"total_cases\": 3668, \"tests\": 22969, \"total_cases_100k\": 342.0761072708892, \"tests_100k\": 2142.0790915771686, \"dead_100k\": 31.98803293181979}, {\"date\": \"2020-04-04T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 644, \"intensive_care\": 142, \"total_hospitalised\": 786, \"home_confinement\": 2168, \"total_positive\": 2954, \"new_current_positive\": 86, \"new_positive\": 144, \"recovered\": 502, \"dead\": 356, \"total_cases\": 3812, \"tests\": 24908, \"total_cases_100k\": 355.5054855279797, \"tests_100k\": 2322.9094001917415, \"dead_100k\": 33.20040735780713}, {\"date\": \"2020-04-05T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 591, \"intensive_care\": 133, \"total_hospitalised\": 724, \"home_confinement\": 2297, \"total_positive\": 3021, \"new_current_positive\": 67, \"new_positive\": 117, \"recovered\": 533, \"dead\": 375, \"total_cases\": 3929, \"tests\": 26199, \"total_cases_100k\": 366.4168553618658, \"tests_100k\": 2443.307506649407, \"dead_100k\": 34.97233921117324}, {\"date\": \"2020-04-06T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 599, \"intensive_care\": 131, \"total_hospitalised\": 730, \"home_confinement\": 2368, \"total_positive\": 3098, \"new_current_positive\": 77, \"new_positive\": 141, \"recovered\": 578, \"dead\": 394, \"total_cases\": 4070, \"tests\": 27955, \"total_cases_100k\": 379.56645490526694, \"tests_100k\": 2607.071313728928, \"dead_100k\": 36.744271064539355}, {\"date\": \"2020-04-07T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 685, \"intensive_care\": 142, \"total_hospitalised\": 827, \"home_confinement\": 2364, \"total_positive\": 3191, \"new_current_positive\": 93, \"new_positive\": 217, \"recovered\": 678, \"dead\": 418, \"total_cases\": 4287, \"tests\": 29791, \"total_cases_100k\": 399.80378186213255, \"tests_100k\": 2778.295886506832, \"dead_100k\": 38.982500774054444}, {\"date\": \"2020-04-08T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 622, \"intensive_care\": 142, \"total_hospitalised\": 764, \"home_confinement\": 2457, \"total_positive\": 3221, \"new_current_positive\": 30, \"new_positive\": 150, \"recovered\": 778, \"dead\": 438, \"total_cases\": 4437, \"tests\": 32123, \"total_cases_100k\": 413.7927175466018, \"tests_100k\": 2995.777206614715, \"dead_100k\": 40.84769219865035}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.FacetChart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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": [
+ "# Total cases and deaths per 100k population\n",
+ "\n",
+ "base = alt.Chart(df_regions).encode(alt.X('date'))\n",
+ "death = base.mark_line(color='black').encode(alt.Y('dead', title='Deaths'))\n",
+ "total = base.mark_bar(color='orange', size=5).encode(alt.Y('total_cases', title=\"Total cases\")).properties(\n",
+ " width=150,\n",
+ " height=150)\n",
+ "totals = alt.layer(total, death)\n",
+ "chart = totals.facet(facet='region', \n",
+ " columns=5, \n",
+ " align='each', \n",
+ " title='Total cases (orange) and deaths (black) by region'\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "metadata": {
+ "papermill": {
+ "duration": 0.18745,
+ "end_time": "2020-04-10T10:55:04.969752",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:04.782302",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-d1128ea2def2441594588e065a899aa1\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-d1128ea2def2441594588e065a899aa1\");\n",
+ " const paths = {\n",
+ " \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
+ " \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
+ " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
+ " };\n",
+ "\n",
+ " function loadScript(lib) {\n",
+ " return new Promise(function(resolve, reject) {\n",
+ " var s = document.createElement('script');\n",
+ " s.src = paths[lib];\n",
+ " s.async = true;\n",
+ " s.onload = () => resolve(paths[lib]);\n",
+ " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
+ " });\n",
+ " }\n",
+ "\n",
+ " function showError(err) {\n",
+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
+ " throw err;\n",
+ " }\n",
+ "\n",
+ " function displayChart(vegaEmbed) {\n",
+ " vegaEmbed(outputDiv, spec, embedOpt)\n",
+ " .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
+ " }\n",
+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"data\": {\"name\": \"data-1302be15f303e6683aab8d2ebee99814\"}, \"facet\": {\"type\": \"nominal\", \"field\": \"region\"}, \"spec\": {\"layer\": [{\"mark\": {\"type\": \"bar\", \"color\": \"orange\", \"size\": 5}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases_100k\", \"title\": \"Total cases\"}}, \"height\": 150, \"width\": 150}, {\"mark\": {\"type\": \"line\", \"color\": \"black\"}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"dead_100k\", \"title\": \"Deaths\"}}}]}, \"align\": \"each\", \"columns\": 5, \"title\": \"Total cases (orange) and deaths (black) by region per 100k population\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-1302be15f303e6683aab8d2ebee99814\": [{\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"region\": \"Abruzzo\", \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 5, \"total_cases_100k\": 0.0, \"tests_100k\": 0.3821312376237246, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 17, \"region\": \"Basilicata\", \"latitude\": 40.63947052, \"longitude\": 15.80514834, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 0, \"total_cases_100k\": 0.0, \"tests_100k\": 0.0, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 18, \"region\": \"Calabria\", \"latitude\": 38.90597598, \"longitude\": 16.59440194, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 1, \"total_cases_100k\": 0.0, \"tests_100k\": 0.05135761281598413, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 15, \"region\": \"Campania\", \"latitude\": 40.83956555, \"longitude\": 14.25084984, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 10, \"total_cases_100k\": 0.0, \"tests_100k\": 0.17035876704545938, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 8, \"region\": \"Emilia-Romagna\", \"latitude\": 44.49436681, \"longitude\": 11.341720800000001, \"hospitalised_with_symptoms\": 10, \"intensive_care\": 2, \"total_hospitalised\": 12, \"home_confinement\": 6, \"total_positive\": 18, \"new_current_positive\": 0, \"new_positive\": 18, \"recovered\": 0, \"dead\": 0, \"total_cases\": 18, \"tests\": 148, \"total_cases_100k\": 0.4036347760062447, \"tests_100k\": 3.318774824940234, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 6, \"region\": \"Friuli Venezia Giulia\", \"latitude\": 45.6494354, \"longitude\": 13.76813649, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 58, \"total_cases_100k\": 0.0, \"tests_100k\": 4.7727983410411285, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 12, \"region\": \"Lazio\", \"latitude\": 41.89277044, \"longitude\": 12.48366722, \"hospitalised_with_symptoms\": 1, \"intensive_care\": 1, \"total_hospitalised\": 2, \"home_confinement\": 0, \"total_positive\": 2, \"new_current_positive\": 0, \"new_positive\": 2, \"recovered\": 1, \"dead\": 0, \"total_cases\": 3, \"tests\": 124, \"total_cases_100k\": 0.051028374838112484, \"tests_100k\": 2.1091728266419825, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 7, \"region\": \"Liguria\", \"latitude\": 44.41149315, \"longitude\": 8.9326992, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 1, \"total_cases_100k\": 0.0, \"tests_100k\": 0.06448950110921942, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 3, \"region\": \"Lombardia\", \"latitude\": 45.46679409, \"longitude\": 9.190347404, \"hospitalised_with_symptoms\": 76, \"intensive_care\": 19, \"total_hospitalised\": 95, \"home_confinement\": 71, \"total_positive\": 166, \"new_current_positive\": 0, \"new_positive\": 166, \"recovered\": 0, \"dead\": 6, \"total_cases\": 172, \"tests\": 1463, \"total_cases_100k\": 1.7084688602744638, \"tests_100k\": 14.531918270822908, \"dead_100k\": 0.05959775093980687}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 11, \"region\": \"Marche\", \"latitude\": 43.61675973, \"longitude\": 13.5188753, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 16, \"total_cases_100k\": 0.0, \"tests_100k\": 1.0508285783340163, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 14, \"region\": \"Molise\", \"latitude\": 41.55774754, \"longitude\": 14.65916051, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 0, \"total_cases_100k\": 0.0, \"tests_100k\": 0.0, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 1, \"region\": \"Piemonte\", \"latitude\": 45.0732745, \"longitude\": 7.680687483, \"hospitalised_with_symptoms\": 2, \"intensive_care\": 0, \"total_hospitalised\": 2, \"home_confinement\": 1, \"total_positive\": 3, \"new_current_positive\": 0, \"new_positive\": 3, \"recovered\": 0, \"dead\": 0, \"total_cases\": 3, \"tests\": 141, \"total_cases_100k\": 0.0688641049525687, \"tests_100k\": 3.236612932770729, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 16, \"region\": \"Puglia\", \"latitude\": 41.12559576, \"longitude\": 16.86736689, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 0, \"total_cases_100k\": 0.0, \"tests_100k\": 0.0, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 20, \"region\": \"Sardegna\", \"latitude\": 39.21531192, \"longitude\": 9.110616306, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 1, \"total_cases_100k\": 0.0, \"tests_100k\": 0.06099082027164091, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 19, \"region\": \"Sicilia\", \"latitude\": 38.11569725, \"longitude\": 13.362356699999998, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, \"total_cases\": 0, \"tests\": 5, \"total_cases_100k\": 0.0, \"tests_100k\": 0.10033153552599208, \"dead_100k\": 0.0}, {\"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 9, \"region\": \"Toscana\", \"latitude\": 43.76923077, \"longitude\": 11.25588885, \"hospitalised_with_symptoms\": 0, \"intensive_care\": 0, \"total_hospitalised\": 0, \"home_confinement\": 0, \"total_positive\": 0, \"new_current_positive\": 0, \"new_positive\": 0, \"recovered\": 0, \"dead\": 0, 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\"ITA\", \"region_code\": 4, \"region\": \"Trentino Alto Adige\", \"latitude\": 46.4337, \"longitude\": 11.1693, \"hospitalised_with_symptoms\": 622, \"intensive_care\": 142, \"total_hospitalised\": 764, \"home_confinement\": 2457, \"total_positive\": 3221, \"new_current_positive\": 30, \"new_positive\": 150, \"recovered\": 778, \"dead\": 438, \"total_cases\": 4437, \"tests\": 32123, \"total_cases_100k\": 413.7927175466018, \"tests_100k\": 2995.777206614715, \"dead_100k\": 40.84769219865035}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.FacetChart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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": [
+ "# Total cases and deaths per 100k population\n",
+ "\n",
+ "base = alt.Chart(df_regions).encode(alt.X('date'))\n",
+ "death = base.mark_line(color='black').encode(alt.Y('dead_100k', title='Deaths'))\n",
+ "total = base.mark_bar(color='orange', size=5).encode(alt.Y('total_cases_100k', title=\"Total cases\")).properties(\n",
+ " width=150,\n",
+ " height=150)\n",
+ "totals = alt.layer(total, death)\n",
+ "chart = totals.facet(facet='region', \n",
+ " columns=5, \n",
+ " align='each', \n",
+ " title='Total cases (orange) and deaths (black) by region per 100k population'\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "metadata": {
+ "papermill": {
+ "duration": 0.117719,
+ "end_time": "2020-04-10T10:55:05.126702",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:05.008983",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": [
+ "# compute daily differences\n",
+ "tdf = df_regions.sort_values(['region', 'date'], ascending=[True, False]).set_index(['region', 'date'])\n",
+ "diffs_df = tdf[['total_cases', 'dead']].groupby(level='region').diff(periods=-1).dropna(how='all')\n",
+ "tdf_diff=tdf.join(diffs_df, rsuffix='_diff').reset_index()\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "metadata": {
+ "papermill": {
+ "duration": 0.198615,
+ "end_time": "2020-04-10T10:55:05.373997",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:05.175382",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-2339034e5e08409b88d480781ef71168\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-2339034e5e08409b88d480781ef71168\");\n",
+ " const paths = {\n",
+ " \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
+ " \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
+ " \"vega-lite\": \"https://cdn.jsdelivr.net/npm//vega-lite@4.0.2?noext\",\n",
+ " \"vega-embed\": \"https://cdn.jsdelivr.net/npm//vega-embed@6?noext\",\n",
+ " };\n",
+ "\n",
+ " function loadScript(lib) {\n",
+ " return new Promise(function(resolve, reject) {\n",
+ " var s = document.createElement('script');\n",
+ " s.src = paths[lib];\n",
+ " s.async = true;\n",
+ " s.onload = () => resolve(paths[lib]);\n",
+ " s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
+ " document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
+ " });\n",
+ " }\n",
+ "\n",
+ " function showError(err) {\n",
+ " outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
+ " throw err;\n",
+ " }\n",
+ "\n",
+ " function displayChart(vegaEmbed) {\n",
+ " vegaEmbed(outputDiv, spec, embedOpt)\n",
+ " .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
+ " }\n",
+ "\n",
+ " if(typeof define === \"function\" && define.amd) {\n",
+ " requirejs.config({paths});\n",
+ " require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
+ " } else if (typeof vegaEmbed === \"function\") {\n",
+ " displayChart(vegaEmbed);\n",
+ " } else {\n",
+ " loadScript(\"vega\")\n",
+ " .then(() => loadScript(\"vega-lite\"))\n",
+ " .then(() => loadScript(\"vega-embed\"))\n",
+ " .catch(showError)\n",
+ " .then(() => displayChart(vegaEmbed));\n",
+ " }\n",
+ " })({\"config\": {\"view\": {\"continuousWidth\": 400, \"continuousHeight\": 300}, \"title\": {\"anchor\": \"middle\"}}, \"data\": {\"name\": \"data-a744c457c9bc9875636e820333778d45\"}, \"facet\": {\"type\": \"nominal\", \"field\": \"region\"}, \"spec\": {\"layer\": [{\"mark\": {\"type\": \"bar\", \"color\": \"orange\"}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"total_cases_diff\", \"title\": \"N\"}}, \"height\": 150, \"width\": 150}, {\"mark\": {\"type\": \"line\", \"color\": \"black\"}, \"encoding\": {\"x\": {\"type\": \"temporal\", \"field\": \"date\"}, \"y\": {\"type\": \"quantitative\", \"field\": \"dead_diff\"}}, \"height\": 150, \"width\": 150}]}, \"align\": \"each\", \"columns\": 5, \"title\": \"Daily new cases (orange) and deaths (black) by region\", \"$schema\": \"https://vega.github.io/schema/vega-lite/v4.0.2.json\", \"datasets\": {\"data-a744c457c9bc9875636e820333778d45\": [{\"region\": \"Abruzzo\", \"date\": \"2020-04-08T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 331, \"intensive_care\": 62, \"total_hospitalised\": 393, \"home_confinement\": 1141, \"total_positive\": 1534, \"new_current_positive\": 43, \"new_positive\": 60, \"recovered\": 146, \"dead\": 179, \"total_cases\": 1859, \"tests\": 15846, \"total_cases_100k\": 142.07639414850078, \"tests_100k\": 1211.0503182771079, \"dead_100k\": 13.68029830692934, \"total_cases_diff\": 60.0, \"dead_diff\": 7.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-04-07T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 337, \"intensive_care\": 67, \"total_hospitalised\": 404, \"home_confinement\": 1087, \"total_positive\": 1491, \"new_current_positive\": 66, \"new_positive\": 78, \"recovered\": 136, \"dead\": 172, \"total_cases\": 1799, \"tests\": 14904, \"total_cases_100k\": 137.4908192970161, \"tests_100k\": 1139.0567931087983, \"dead_100k\": 13.145314574256124, \"total_cases_diff\": 78.0, \"dead_diff\": 3.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-04-06T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 340, \"intensive_care\": 66, \"total_hospitalised\": 406, \"home_confinement\": 1019, \"total_positive\": 1425, \"new_current_positive\": 5, \"new_positive\": 18, \"recovered\": 127, \"dead\": 169, \"total_cases\": 1721, \"tests\": 14198, \"total_cases_100k\": 131.52957199008597, \"tests_100k\": 1085.0998623563282, \"dead_100k\": 12.916035831681889, \"total_cases_diff\": 18.0, \"dead_diff\": 11.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-04-05T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 347, \"intensive_care\": 67, \"total_hospitalised\": 414, \"home_confinement\": 1006, \"total_positive\": 1420, \"new_current_positive\": 64, \"new_positive\": 75, \"recovered\": 125, \"dead\": 158, \"total_cases\": 1703, \"tests\": 13598, \"total_cases_100k\": 130.15389953464057, \"tests_100k\": 1039.2441138414813, \"dead_100k\": 12.075347108909696, \"total_cases_diff\": 75.0, \"dead_diff\": 5.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-04-04T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 354, \"intensive_care\": 71, \"total_hospitalised\": 425, \"home_confinement\": 931, \"total_positive\": 1356, \"new_current_positive\": 55, \"new_positive\": 65, \"recovered\": 119, \"dead\": 153, \"total_cases\": 1628, \"tests\": 12837, \"total_cases_100k\": 124.4219309702847, \"tests_100k\": 981.0837394751503, \"dead_100k\": 11.69321587128597, \"total_cases_diff\": 65.0, \"dead_diff\": 7.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-04-03T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 361, \"intensive_care\": 76, \"total_hospitalised\": 437, \"home_confinement\": 864, \"total_positive\": 1301, \"new_current_positive\": 50, \"new_positive\": 66, \"recovered\": 116, \"dead\": 146, \"total_cases\": 1563, \"tests\": 11890, \"total_cases_100k\": 119.45422488117629, \"tests_100k\": 908.7080830692171, \"dead_100k\": 11.158232138612757, \"total_cases_diff\": 66.0, \"dead_diff\": 13.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-04-02T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 341, \"intensive_care\": 75, \"total_hospitalised\": 416, \"home_confinement\": 835, \"total_positive\": 1251, \"new_current_positive\": 40, \"new_positive\": 61, \"recovered\": 113, \"dead\": 133, \"total_cases\": 1497, \"tests\": 10647, \"total_cases_100k\": 114.41009254454313, \"tests_100k\": 813.710257395959, \"dead_100k\": 10.164690920791072, \"total_cases_diff\": 61.0, \"dead_diff\": 10.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-04-01T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 342, \"intensive_care\": 71, \"total_hospitalised\": 413, \"home_confinement\": 798, \"total_positive\": 1211, \"new_current_positive\": 20, \"new_positive\": 35, \"recovered\": 102, \"dead\": 123, \"total_cases\": 1436, \"tests\": 9610, \"total_cases_100k\": 109.74809144553369, \"tests_100k\": 734.4562387127986, \"dead_100k\": 9.400428445543623, \"total_cases_diff\": 35.0, \"dead_diff\": 8.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-03-31T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 335, \"intensive_care\": 73, \"total_hospitalised\": 408, \"home_confinement\": 783, \"total_positive\": 1191, \"new_current_positive\": 22, \"new_positive\": 56, \"recovered\": 95, \"dead\": 115, \"total_cases\": 1401, \"tests\": 8758, \"total_cases_100k\": 107.0731727821676, \"tests_100k\": 669.3410758217159, \"dead_100k\": 8.789018465345665, \"total_cases_diff\": 56.0, \"dead_diff\": 13.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-03-30T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 322, \"intensive_care\": 69, \"total_hospitalised\": 391, \"home_confinement\": 778, \"total_positive\": 1169, \"new_current_positive\": 0, \"new_positive\": 52, \"recovered\": 74, \"dead\": 102, \"total_cases\": 1345, \"tests\": 7948, \"total_cases_100k\": 102.79330292078191, \"tests_100k\": 607.4358153266725, \"dead_100k\": 7.79547724752398, \"total_cases_diff\": 52.0, \"dead_diff\": 14.0}, {\"region\": 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\"2020-03-24T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 234, \"intensive_care\": 57, \"total_hospitalised\": 291, \"home_confinement\": 331, \"total_positive\": 622, \"new_current_positive\": 17, \"new_positive\": 26, \"recovered\": 21, \"dead\": 46, \"total_cases\": 689, \"tests\": 4294, \"total_cases_100k\": 52.65768454454924, \"tests_100k\": 328.1743068712546, \"dead_100k\": 3.515607386138266, \"total_cases_diff\": 26.0, \"dead_diff\": 8.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-03-23T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 228, \"intensive_care\": 52, \"total_hospitalised\": 280, \"home_confinement\": 325, \"total_positive\": 605, \"new_current_positive\": 66, \"new_positive\": 76, \"recovered\": 20, \"dead\": 38, \"total_cases\": 663, \"tests\": 3674, \"total_cases_100k\": 50.670602108905875, \"tests_100k\": 280.79003340591277, \"dead_100k\": 2.904197405940306, \"total_cases_diff\": 76.0, \"dead_diff\": 5.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-03-22T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 218, \"intensive_care\": 49, \"total_hospitalised\": 267, \"home_confinement\": 272, \"total_positive\": 539, \"new_current_positive\": 45, \"new_positive\": 58, \"recovered\": 15, \"dead\": 33, \"total_cases\": 587, \"tests\": 3375, \"total_cases_100k\": 44.86220729702526, \"tests_100k\": 257.93858539601405, \"dead_100k\": 2.5220661683165817, \"total_cases_diff\": 58.0, \"dead_diff\": 11.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-03-21T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 185, \"intensive_care\": 44, \"total_hospitalised\": 229, \"home_confinement\": 265, \"total_positive\": 494, \"new_current_positive\": 72, \"new_positive\": 80, \"recovered\": 13, \"dead\": 22, \"total_cases\": 529, \"tests\": 3035, \"total_cases_100k\": 40.42948494059006, \"tests_100k\": 231.9536612376008, \"dead_100k\": 1.681377445544388, \"total_cases_diff\": 80.0, \"dead_diff\": 5.0}, {\"region\": \"Abruzzo\", \"date\": \"2020-03-20T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 13, \"latitude\": 42.35122196, \"longitude\": 13.39843823, \"hospitalised_with_symptoms\": 190, \"intensive_care\": 48, \"total_hospitalised\": 238, \"home_confinement\": 184, \"total_positive\": 422, \"new_current_positive\": 56, \"new_positive\": 64, \"recovered\": 10, \"dead\": 17, \"total_cases\": 449, \"tests\": 2695, \"total_cases_100k\": 34.315385138610466, \"tests_100k\": 205.96873707918752, \"dead_100k\": 1.2992462079206635, \"total_cases_diff\": 64.0, \"dead_diff\": 6.0}, {\"region\": \"Abruzzo\", \"date\": 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\"date\": \"2020-03-18T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 646, \"intensive_care\": 195, \"total_hospitalised\": 841, \"home_confinement\": 2112, \"total_positive\": 2953, \"new_current_positive\": 465, \"new_positive\": 510, \"recovered\": 167, \"dead\": 94, \"total_cases\": 3214, \"tests\": 40841, \"total_cases_100k\": 65.2348026657368, \"tests_100k\": 828.9528860209571, \"dead_100k\": 1.9079251557496135, \"total_cases_diff\": 510.0, \"dead_diff\": 14.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-17T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 548, \"intensive_care\": 171, \"total_hospitalised\": 719, \"home_confinement\": 1769, \"total_positive\": 2488, \"new_current_positive\": 214, \"new_positive\": 231, \"recovered\": 136, \"dead\": 80, \"total_cases\": 2704, \"tests\": 35478, \"total_cases_100k\": 54.88329384198889, \"tests_100k\": 720.0996667626041, \"dead_100k\": 1.623766089999671, \"total_cases_diff\": 231.0, \"dead_diff\": 11.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-16T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 498, \"intensive_care\": 156, \"total_hospitalised\": 654, \"home_confinement\": 1620, \"total_positive\": 2274, \"new_current_positive\": 285, \"new_positive\": 301, \"recovered\": 130, \"dead\": 69, \"total_cases\": 2473, \"tests\": 35052, \"total_cases_100k\": 50.19466925711484, \"tests_100k\": 711.4531123333559, \"dead_100k\": 1.4004982526247163, \"total_cases_diff\": 301.0, \"dead_diff\": 6.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-15T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 426, \"intensive_care\": 129, \"total_hospitalised\": 555, \"home_confinement\": 1434, \"total_positive\": 1989, \"new_current_positive\": 214, \"new_positive\": 235, \"recovered\": 120, \"dead\": 63, \"total_cases\": 2172, \"tests\": 32546, \"total_cases_100k\": 44.08524934349107, \"tests_100k\": 660.5886395641162, \"dead_100k\": 1.278715795874741, \"total_cases_diff\": 235.0, \"dead_diff\": 8.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-14T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 366, \"intensive_care\": 119, \"total_hospitalised\": 485, \"home_confinement\": 1290, \"total_positive\": 1775, \"new_current_positive\": 322, \"new_positive\": 342, \"recovered\": 107, \"dead\": 55, \"total_cases\": 1937, \"tests\": 26980, \"total_cases_100k\": 39.31543645411704, \"tests_100k\": 547.6151138523892, \"dead_100k\": 1.1163391868747738, \"total_cases_diff\": 342.0, \"dead_diff\": 13.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-13T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 366, \"intensive_care\": 107, \"total_hospitalised\": 473, \"home_confinement\": 980, \"total_positive\": 1453, \"new_current_positive\": 156, \"new_positive\": 211, \"recovered\": 100, \"dead\": 42, \"total_cases\": 1595, \"tests\": 25691, \"total_cases_100k\": 32.373836419368445, \"tests_100k\": 521.4521827272694, \"dead_100k\": 0.8524771972498274, \"total_cases_diff\": 211.0, \"dead_diff\": 10.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-12T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 360, \"intensive_care\": 85, \"total_hospitalised\": 445, \"home_confinement\": 852, \"total_positive\": 1297, \"new_current_positive\": 357, \"new_positive\": 361, \"recovered\": 55, \"dead\": 32, \"total_cases\": 1384, \"tests\": 23438, \"total_cases_100k\": 28.09115335699431, \"tests_100k\": 475.7228702176537, \"dead_100k\": 0.6495064359998685, \"total_cases_diff\": 361.0, \"dead_diff\": 3.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-11T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 262, \"intensive_care\": 68, \"total_hospitalised\": 330, \"home_confinement\": 610, \"total_positive\": 940, \"new_current_positive\": 157, \"new_positive\": 167, \"recovered\": 54, \"dead\": 29, \"total_cases\": 1023, \"tests\": 21400, \"total_cases_100k\": 20.763908875870793, \"tests_100k\": 434.35742907491203, \"dead_100k\": 0.5886152076248808, \"total_cases_diff\": 167.0, \"dead_diff\": 3.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-10T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 204, \"intensive_care\": 67, \"total_hospitalised\": 271, \"home_confinement\": 512, \"total_positive\": 783, \"new_current_positive\": 89, \"new_positive\": 112, \"recovered\": 47, \"dead\": 26, \"total_cases\": 856, \"tests\": 16643, \"total_cases_100k\": 17.37429716299648, \"tests_100k\": 337.8042379483066, \"dead_100k\": 0.5277239792498931, \"total_cases_diff\": 112.0, \"dead_diff\": 6.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-09T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 186, \"intensive_care\": 51, \"total_hospitalised\": 237, \"home_confinement\": 457, \"total_positive\": 694, \"new_current_positive\": 71, \"new_positive\": 74, \"recovered\": 30, \"dead\": 20, \"total_cases\": 744, \"tests\": 15956, \"total_cases_100k\": 15.101024636996941, \"tests_100k\": 323.8601466504344, \"dead_100k\": 0.4059415224999178, \"total_cases_diff\": 74.0, \"dead_diff\": 2.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-08T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 146, \"intensive_care\": 47, \"total_hospitalised\": 193, \"home_confinement\": 430, \"total_positive\": 623, \"new_current_positive\": 118, \"new_positive\": 127, \"recovered\": 29, \"dead\": 18, \"total_cases\": 670, \"tests\": 15918, \"total_cases_100k\": 13.599041003747246, \"tests_100k\": 323.08885775768454, \"dead_100k\": 0.36534737024992603, \"total_cases_diff\": 127.0, \"dead_diff\": 5.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-07T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 123, \"intensive_care\": 41, \"total_hospitalised\": 164, \"home_confinement\": 341, \"total_positive\": 505, \"new_current_positive\": 51, \"new_positive\": 55, \"recovered\": 25, \"dead\": 13, \"total_cases\": 543, \"tests\": 14429, \"total_cases_100k\": 11.021312335872768, \"tests_100k\": 292.86651140756567, \"dead_100k\": 0.26386198962494656, \"total_cases_diff\": 55.0, \"dead_diff\": 1.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-06T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 117, \"intensive_care\": 27, \"total_hospitalised\": 144, \"home_confinement\": 310, \"total_positive\": 454, \"new_current_positive\": 74, \"new_positive\": 81, \"recovered\": 22, \"dead\": 12, \"total_cases\": 488, \"tests\": 13023, \"total_cases_100k\": 9.904973148997994, \"tests_100k\": 264.32882237582146, \"dead_100k\": 0.24356491349995066, \"total_cases_diff\": 81.0, \"dead_diff\": 2.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-05T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 92, \"intensive_care\": 24, \"total_hospitalised\": 116, \"home_confinement\": 264, \"total_positive\": 380, \"new_current_positive\": 35, \"new_positive\": 47, \"recovered\": 17, \"dead\": 10, \"total_cases\": 407, \"tests\": 11949, \"total_cases_100k\": 8.260909982873327, \"tests_100k\": 242.52976261757587, \"dead_100k\": 0.2029707612499589, \"total_cases_diff\": 47.0, \"dead_diff\": 4.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-04T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 76, \"intensive_care\": 23, \"total_hospitalised\": 99, \"home_confinement\": 246, \"total_positive\": 345, \"new_current_positive\": 48, \"new_positive\": 53, \"recovered\": 9, \"dead\": 6, \"total_cases\": 360, \"tests\": 10515, \"total_cases_100k\": 7.306947404998521, \"tests_100k\": 213.42375545433177, \"dead_100k\": 0.12178245674997533, \"total_cases_diff\": 53.0, \"dead_diff\": 3.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-03T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 49, \"intensive_care\": 19, \"total_hospitalised\": 68, \"home_confinement\": 229, \"total_positive\": 297, \"new_current_positive\": 26, \"new_positive\": 34, \"recovered\": 7, \"dead\": 3, \"total_cases\": 307, \"tests\": 10176, \"total_cases_100k\": 6.2312023703737385, \"tests_100k\": 206.54304664795816, \"dead_100k\": 0.060891228374987665, \"total_cases_diff\": 34.0, \"dead_diff\": 1.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-02T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 53, \"intensive_care\": 14, \"total_hospitalised\": 67, \"home_confinement\": 204, \"total_positive\": 271, \"new_current_positive\": 10, \"new_positive\": 10, \"recovered\": 0, \"dead\": 2, \"total_cases\": 273, \"tests\": 9782, \"total_cases_100k\": 5.541101782123878, \"tests_100k\": 198.54599865470982, \"dead_100k\": 0.04059415224999178, \"total_cases_diff\": 10.0, \"dead_diff\": 0.0}, {\"region\": \"Veneto\", \"date\": \"2020-03-01T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 51, \"intensive_care\": 13, \"total_hospitalised\": 64, \"home_confinement\": 197, \"total_positive\": 261, \"new_current_positive\": 72, \"new_positive\": 72, \"recovered\": 0, \"dead\": 2, \"total_cases\": 263, \"tests\": 9056, \"total_cases_100k\": 5.338131020873919, \"tests_100k\": 183.81032138796277, \"dead_100k\": 0.04059415224999178, \"total_cases_diff\": 72.0, \"dead_diff\": 0.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-29T17:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 24, \"intensive_care\": 11, \"total_hospitalised\": 35, \"home_confinement\": 154, \"total_positive\": 189, \"new_current_positive\": 40, \"new_positive\": 40, \"recovered\": 0, \"dead\": 2, \"total_cases\": 191, \"tests\": 8659, \"total_cases_100k\": 3.8767415398742147, \"tests_100k\": 175.75238216633943, \"dead_100k\": 0.04059415224999178, \"total_cases_diff\": 40.0, \"dead_diff\": 0.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-28T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 24, \"intensive_care\": 9, \"total_hospitalised\": 33, \"home_confinement\": 116, \"total_positive\": 149, \"new_current_positive\": 40, \"new_positive\": 40, \"recovered\": 0, \"dead\": 2, \"total_cases\": 151, \"tests\": 7414, \"total_cases_100k\": 3.06485849487438, \"tests_100k\": 150.48252239071954, \"dead_100k\": 0.04059415224999178, \"total_cases_diff\": 40.0, \"dead_diff\": 0.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-27T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 19, \"intensive_care\": 8, \"total_hospitalised\": 27, \"home_confinement\": 82, \"total_positive\": 109, \"new_current_positive\": 40, \"new_positive\": 40, \"recovered\": 0, \"dead\": 2, \"total_cases\": 111, \"tests\": 6164, \"total_cases_100k\": 2.2529754498745436, \"tests_100k\": 125.11117723447467, \"dead_100k\": 0.04059415224999178, \"total_cases_diff\": 40.0, \"dead_diff\": 0.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-26T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 16, \"intensive_care\": 8, \"total_hospitalised\": 24, \"home_confinement\": 45, \"total_positive\": 69, \"new_current_positive\": 27, \"new_positive\": 28, \"recovered\": 0, \"dead\": 2, \"total_cases\": 71, \"tests\": 4900, \"total_cases_100k\": 1.4410924048747082, \"tests_100k\": 99.45567301247986, \"dead_100k\": 0.04059415224999178, \"total_cases_diff\": 28.0, \"dead_diff\": 1.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-25T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 12, \"intensive_care\": 7, \"total_hospitalised\": 19, \"home_confinement\": 23, \"total_positive\": 42, \"new_current_positive\": 10, \"new_positive\": 10, \"recovered\": 0, \"dead\": 1, \"total_cases\": 43, \"tests\": 3780, \"total_cases_100k\": 0.8727742733748233, \"tests_100k\": 76.72294775248447, \"dead_100k\": 0.02029707612499589, \"total_cases_diff\": 10.0, \"dead_diff\": 0.0}, {\"region\": \"Veneto\", \"date\": \"2020-02-24T18:00:00\", \"country_code\": \"ITA\", \"region_code\": 5, \"latitude\": 45.43490485, \"longitude\": 12.33845213, \"hospitalised_with_symptoms\": 12, \"intensive_care\": 4, \"total_hospitalised\": 16, \"home_confinement\": 16, \"total_positive\": 32, \"new_current_positive\": 0, \"new_positive\": 32, \"recovered\": 0, \"dead\": 1, \"total_cases\": 33, \"tests\": 2200, \"total_cases_100k\": 0.6698035121248644, \"tests_100k\": 44.65356747499096, \"dead_100k\": 0.02029707612499589, \"total_cases_diff\": null, \"dead_diff\": null}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.FacetChart(...)"
+ ]
+ },
+ "metadata": {},
+ "output_type": "display_data"
+ },
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<p style=\"font-size: smaller\">Data Sources: \n",
+ " <a href=\"https://github.com/pcm-dpc/COVID-19\">Italian Civil Protection</a>, <a href=\"https://wikidata.org\">Wikidata</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": [
+ "# make the daily charts\n",
+ "base = alt.Chart(tdf_diff).encode(alt.X('date')).properties(\n",
+ " width=150,\n",
+ " height=150,\n",
+ ")\n",
+ "daily_new = base.mark_bar(color='orange').encode(alt.Y('total_cases_diff', title='N'))\n",
+ "daily_dead = base.mark_line(color='black').encode(alt.Y('dead_diff'))\n",
+ "chart = (daily_new + daily_dead).facet(\n",
+ " facet='region', \n",
+ " columns=5, \n",
+ " align='each', \n",
+ " title='Daily new cases (orange) and deaths (black) by region',\n",
+ ").configure_title(\n",
+ " anchor='middle'\n",
+ ")\n",
+ "display(chart)\n",
+ "display(html_credits)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "papermill": {
+ "duration": 0.053259,
+ "end_time": "2020-04-10T10:55:05.479482",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:05.426223",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": []
+ },
+ {
+ "cell_type": "markdown",
+ "metadata": {
+ "papermill": {
+ "duration": 0.052853,
+ "end_time": "2020-04-10T10:55:05.586900",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:05.534047",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "source": [
+ "## Rates of growth\n",
+ "\n",
+ "How quickly is the infection spreading? The charts below show data for all of the regions of Italy framed by some illustrative guiding lines to give an idea of how the rate of infection is evolving. "
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "metadata": {
+ "papermill": {
+ "duration": 0.320977,
+ "end_time": "2020-04-10T10:55:05.958483",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:05.637506",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-73ad778ca13a413fadfa652121da5da6\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-73ad778ca13a413fadfa652121da5da6\");\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",
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28718, \"intensive_care\": 3792, \"total_hospitalised\": 32510, \"home_confinement\": 61557, \"total_positive\": 94067, \"new_current_positive\": 880, \"new_positive\": 3039, \"recovered\": 24392, \"dead\": 17127, \"total_cases\": 135586, \"tests\": 755445, \"New cases per day\": 3039.0, \"sinceDay0\": 43, \"country_label\": \"Italy\"}, {\"index\": 44, \"date\": \"2020-04-08T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28485, \"intensive_care\": 3693, \"total_hospitalised\": 32178, \"home_confinement\": 63084, \"total_positive\": 95262, \"new_current_positive\": 1195, \"new_positive\": 3836, \"recovered\": 26491, \"dead\": 17669, \"total_cases\": 139422, \"tests\": 807125, \"New cases per day\": 3836.0, \"sinceDay0\": 44, \"country_label\": \"Italy\"}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 16,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "since_100th_case = helper.make_since_df(df_regions, column='total_cases', region_column='region')\n",
+ "\n",
+ "base = alt.Chart(since_100th_case, title=\"Italy: total cases since 100th case\").mark_line(interpolate='basis')\n",
+ "\n",
+ "line_chart = plotting.make_region_since_chart(\n",
+ " base,\n",
+ " 'total_cases',\n",
+ " 'sinceDay0',\n",
+ " 'region',\n",
+ " 'Days since 100th case',\n",
+ " 'Cumulative cases', \n",
+ " 'Cases',\n",
+ " 'Region'\n",
+ ").properties(\n",
+ " width=450,\n",
+ " height=450\n",
+ ")\n",
+ "\n",
+ "rule_chart = plotting.make_rule_chart(max_case=110000, max_days=40, pos_day=(12,50000), pos_3days=(35,300000), pos_week=(40,2000))\n",
+ "\n",
+ "# add the total cases for italy to the chart\n",
+ "since_100th_case_all = helper.make_since_df(df_national, start_case=100, column='total_cases', region_column='country_code')\n",
+ "since_100th_case_all['country_label'] = 'Italy'\n",
+ "italy = alt.Chart(since_100th_case_all).mark_line(color='steelblue').encode(x='sinceDay0', y='total_cases')\n",
+ "italy += italy.mark_text(dy=-10).encode(text='country_label').transform_filter(f\"datum['sinceDay0'] == {len(since_100th_case_all)-1}\")\n",
+ "\n",
+ "\n",
+ "line_chart + rule_chart + italy"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "metadata": {
+ "papermill": {
+ "duration": 0.319887,
+ "end_time": "2020-04-10T10:55:06.341616",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:06.021729",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ "\n",
+ "<div id=\"altair-viz-ca3e0443fc5049649405ddc1a3f4a37a\"></div>\n",
+ "<script type=\"text/javascript\">\n",
+ " (function(spec, embedOpt){\n",
+ " const outputDiv = document.getElementById(\"altair-viz-ca3e0443fc5049649405ddc1a3f4a37a\");\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}}, \"layer\": [{\"data\": {\"name\": \"data-1a786aff0a68d4adb33db842e726355d\"}, \"mark\": \"line\", \"encoding\": {\"color\": {\"type\": \"nominal\", \"field\": \"region\", \"legend\": {\"title\": \"Region\"}}, \"opacity\": {\"condition\": {\"value\": 1, \"selection\": \"selector002\"}, \"value\": 0.2}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"region\", \"title\": \"Region\"}, {\"type\": \"quantitative\", \"field\": \"dead\", \"title\": \"Deaths\"}, {\"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\": \"dead\", \"scale\": {\"type\": \"log\"}}}, \"height\": 450, \"selection\": {\"selector002\": {\"type\": \"multi\", \"fields\": [\"region\"], \"bind\": \"legend\"}}, \"title\": 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\"ITA\", \"hospitalised_with_symptoms\": 28192, \"intensive_care\": 4023, \"total_hospitalised\": 32215, \"home_confinement\": 45420, \"total_positive\": 77635, \"new_current_positive\": 2107, \"new_positive\": 4053, \"recovered\": 15729, \"dead\": 12428, \"total_cases\": 105792, \"tests\": 506968, \"New cases per day\": 4053.0, \"sinceDay0\": 35, \"country_label\": \"Italy\"}, {\"index\": 37, \"date\": \"2020-04-01T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28403, \"intensive_care\": 4035, \"total_hospitalised\": 32438, \"home_confinement\": 48134, \"total_positive\": 80572, \"new_current_positive\": 2937, \"new_positive\": 4782, \"recovered\": 16847, \"dead\": 13155, \"total_cases\": 110574, \"tests\": 541423, \"New cases per day\": 4782.0, \"sinceDay0\": 36, \"country_label\": \"Italy\"}, {\"index\": 38, \"date\": \"2020-04-02T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28540, \"intensive_care\": 4053, \"total_hospitalised\": 32593, \"home_confinement\": 50456, \"total_positive\": 83049, \"new_current_positive\": 2477, \"new_positive\": 4668, \"recovered\": 18278, \"dead\": 13915, \"total_cases\": 115242, \"tests\": 581232, \"New cases per day\": 4668.0, \"sinceDay0\": 37, \"country_label\": \"Italy\"}, {\"index\": 39, \"date\": \"2020-04-03T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28741, \"intensive_care\": 4068, \"total_hospitalised\": 32809, \"home_confinement\": 52579, \"total_positive\": 85388, \"new_current_positive\": 2339, \"new_positive\": 4585, \"recovered\": 19758, \"dead\": 14681, \"total_cases\": 119827, \"tests\": 619849, \"New cases per day\": 4585.0, \"sinceDay0\": 38, \"country_label\": \"Italy\"}, {\"index\": 40, \"date\": \"2020-04-04T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 29010, \"intensive_care\": 3994, \"total_hospitalised\": 33004, \"home_confinement\": 55270, \"total_positive\": 88274, \"new_current_positive\": 2886, \"new_positive\": 4805, \"recovered\": 20996, \"dead\": 15362, \"total_cases\": 124632, \"tests\": 657224, \"New cases per day\": 4805.0, \"sinceDay0\": 39, \"country_label\": \"Italy\"}, {\"index\": 41, \"date\": \"2020-04-05T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28949, \"intensive_care\": 3977, \"total_hospitalised\": 32926, \"home_confinement\": 58320, \"total_positive\": 91246, \"new_current_positive\": 2972, \"new_positive\": 4316, \"recovered\": 21815, \"dead\": 15887, \"total_cases\": 128948, \"tests\": 691461, \"New cases per day\": 4316.0, \"sinceDay0\": 40, \"country_label\": \"Italy\"}, {\"index\": 42, \"date\": \"2020-04-06T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28976, \"intensive_care\": 3898, \"total_hospitalised\": 32874, \"home_confinement\": 60313, \"total_positive\": 93187, \"new_current_positive\": 1941, \"new_positive\": 3599, \"recovered\": 22837, \"dead\": 16523, \"total_cases\": 132547, \"tests\": 721732, \"New cases per day\": 3599.0, \"sinceDay0\": 41, \"country_label\": \"Italy\"}, {\"index\": 43, \"date\": \"2020-04-07T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28718, \"intensive_care\": 3792, \"total_hospitalised\": 32510, \"home_confinement\": 61557, \"total_positive\": 94067, \"new_current_positive\": 880, \"new_positive\": 3039, \"recovered\": 24392, \"dead\": 17127, \"total_cases\": 135586, \"tests\": 755445, \"New cases per day\": 3039.0, \"sinceDay0\": 42, \"country_label\": \"Italy\"}, {\"index\": 44, \"date\": \"2020-04-08T17:00:00\", \"country_code\": \"ITA\", \"hospitalised_with_symptoms\": 28485, \"intensive_care\": 3693, \"total_hospitalised\": 32178, \"home_confinement\": 63084, \"total_positive\": 95262, \"new_current_positive\": 1195, \"new_positive\": 3836, \"recovered\": 26491, \"dead\": 17669, \"total_cases\": 139422, \"tests\": 807125, \"New cases per day\": 3836.0, \"sinceDay0\": 43, \"country_label\": \"Italy\"}]}}, {\"mode\": \"vega-lite\"});\n",
+ "</script>"
+ ],
+ "text/plain": [
+ "alt.LayerChart(...)"
+ ]
+ },
+ "execution_count": 17,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "since_10th_death = helper.make_since_df(df_regions, start_case=10, column='dead', region_column='region')\n",
+ "\n",
+ "base = alt.Chart(since_10th_death, title=\"Italy: total deaths since 10th death\")\n",
+ "line_chart = plotting.make_region_since_chart(\n",
+ " base,\n",
+ " 'dead',\n",
+ " 'sinceDay0',\n",
+ " 'region',\n",
+ " 'Days since 10th death',\n",
+ " 'Cumulative deaths', \n",
+ " 'Deaths',\n",
+ " 'Region'\n",
+ ").properties(\n",
+ " width=450,\n",
+ " height=450\n",
+ ")\n",
+ "\n",
+ "rule_chart = plotting.make_rule_chart(\n",
+ " start_case=10, \n",
+ " max_case=50000, \n",
+ " max_days=40, \n",
+ " pos_day=(12,50000), \n",
+ " pos_3days=(35,20000), \n",
+ " pos_week=(40,100)) \n",
+ "\n",
+ "\n",
+ "# add the total deaths for italy to the chart\n",
+ "since_10th_death_all = helper.make_since_df(df_national, start_case=10, column='dead', region_column='country_code')\n",
+ "since_10th_death_all['country_label'] = 'Italy'\n",
+ "italy = alt.Chart(since_10th_death_all).mark_line(color='steelblue').encode(x='sinceDay0', y='dead')\n",
+ "italy += italy.mark_text(dy=-10).encode(text='country_label').transform_filter(f\"datum['sinceDay0'] == {len(since_10th_death_all)-1}\")\n",
+ "\n",
+ "line_chart + rule_chart + italy"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {
+ "papermill": {
+ "duration": 0.078121,
+ "end_time": "2020-04-10T10:55:06.495420",
+ "exception": false,
+ "start_time": "2020-04-10T10:55:06.417299",
+ "status": "completed"
+ },
+ "tags": []
+ },
+ "outputs": [],
+ "source": []
+ }
+ ],
+ "metadata": {
+ "hide_input": true,
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 3
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython3",
+ "version": "3.7.3"
+ },
+ "papermill": {
+ "duration": 5.794366,
+ "end_time": "2020-04-10T10:55:06.889044",
+ "environment_variables": {},
+ "exception": null,
+ "input_path": "notebooks/covid-19-italy.ipynb",
+ "output_path": "runs/covid-19-italy.run.ipynb",
+ "parameters": {
+ "data_folder": "./data/covid-19-italy/"
+ },
+ "start_time": "2020-04-10T10:55:01.094678",
+ "version": "1.1.0"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
\ No newline at end of file
--
GitLab