Dashboard.run.ipynb

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   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "import os\n",
    "from IPython.display import display, HTML, Markdown\n",
    "import covid_19_dashboard as helper"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
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     "start_time": "2020-03-21T08:21:34.872190",
     "status": "completed"
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    "tags": [
     "parameters"
    ]
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   "outputs": [],
   "source": [
    "ts_folder = \"../data/covid-19_jhu-csse/\"\n",
    "rates_folder = \"../data/covid-19_rates/\"\n",
    "geodata_path = \"../data/geodata/geo_data.csv\"\n",
    "out_folder = None\n",
    "PAPERMILL_OUTPUT_PATH = None"
   ]
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  {
   "cell_type": "code",
   "execution_count": 3,
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     "start_time": "2020-03-21T08:21:34.905556",
     "status": "completed"
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    "tags": [
     "injected-parameters"
    ]
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   "outputs": [],
   "source": [
    "# Parameters\n",
    "PAPERMILL_INPUT_PATH = \"/tmp/t7uqe0kc/notebooks/Dashboard.ipynb\"\n",
    "PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
    "ts_folder = \"/tmp/t7uqe0kc/data/covid-19_jhu-csse\"\n",
    "rates_folder = \"/tmp/t7uqe0kc/data/covid-19_rates\"\n",
    "geodata_path = \"/tmp/t7uqe0kc/data/geodata/geo_data.csv\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
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     "duration": 0.023145,
     "end_time": "2020-03-21T08:21:34.964505",
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    "tags": []
   },
   "outputs": [],
   "source": [
    "# Read in the data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
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     "status": "completed"
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   "outputs": [],
   "source": [
    "jhu_frames_map = helper.read_jhu_frames_map(ts_folder)\n",
    "rates_frames_map = helper.read_rates_frames_map(rates_folder)\n",
    "geodata_df = helper.read_geodata(geodata_path)\n",
    "\n",
    "# Identify countries with 100 or more cases\n",
    "countries_over_thresh = helper.countries_with_number_of_cases(jhu_frames_map, 'confirmed', 100)\n",
    "# Filter out some countries with very high case/population ratio\n",
    "countries_over_thresh = [c for c in countries_over_thresh if c not in set(['San Marino', 'Iceland'])]"
   ]
  },
  {
   "cell_type": "markdown",
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     "start_time": "2020-03-21T08:21:35.260253",
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    "tags": []
   },
   "source": [
    "# Questions About COVID-19 and Its Spread\n",
    "\n",
    "Understanding the spread, distribution, and deadliness of COVID-19 is difficult, despite the data available about it. Differences in rates of testing, quality of data, demographics, etc. make it difficult to compare data between countries. \n",
    "\n",
    "All this needs to be considered when looking at the plots below. But despite those caveats, I found it helpful to plot the raw data, even though direct comparisons between countries might not be inaccurate."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
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     "duration": 0.035757,
     "end_time": "2020-03-21T08:21:35.321446",
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   "outputs": [
    {
     "data": {
      "text/html": [
       "<em>Data up to Mar 20 2020; countries with 100 or more confirmed cases.</em>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
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     "output_type": "display_data"
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   ],
   "source": [
    "data_ts = jhu_frames_map['confirmed'].iloc[:,-1].name.strftime(\"%b %d %Y\")\n",
    "display(HTML(f\"<em>Data up to {data_ts}; countries with 100 or more confirmed cases.</em>\"))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
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    "tags": []
   },
   "source": [
    "## How are cases per 100,000 distributed geographically?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "papermill": {
     "duration": 0.023769,
     "end_time": "2020-03-21T08:21:35.387608",
     "exception": false,
     "start_time": "2020-03-21T08:21:35.363839",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "import altair as alt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "papermill": {
     "duration": 0.05008,
     "end_time": "2020-03-21T08:21:35.451869",
     "exception": false,
     "start_time": "2020-03-21T08:21:35.401789",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "map_df = helper.compute_map_df(rates_frames_map, jhu_frames_map, geodata_df, countries_over_thresh)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
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     "start_time": "2020-03-21T08:21:35.465541",
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\"Recovered/100k\": 0.0031698034883497197, \"Confirmed\": 164.0, \"Deaths\": 1.0, \"Recovered\": 4.0, \"Long\": -102.52345169, \"Lat\": 23.94753724}, {\"Country/Region\": \"Netherlands\", \"Confirmed/100k\": 14.317204840550039, \"Deaths/100k\": 0.4468685742692959, \"Recovered/100k\": 0.011606975955046644, \"Confirmed\": 3003.0, \"Deaths\": 107.0, \"Recovered\": 2.0, \"Long\": 5.28144793, \"Lat\": 52.1007899}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 32.85452782812378, \"Deaths/100k\": 0.131719183732455, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 1914.0, \"Deaths\": 7.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572}, {\"Country/Region\": \"Pakistan\", \"Confirmed/100k\": 0.213933951803508, \"Deaths/100k\": 0.0009424403163150133, \"Recovered/100k\": 0.006125862056047585, \"Confirmed\": 501.0, \"Deaths\": 3.0, \"Recovered\": 13.0, \"Long\": 69.33957937, \"Lat\": 29.9497515}, {\"Country/Region\": \"Panama\", \"Confirmed/100k\": 2.609607713713105, \"Deaths/100k\": 0.02394135517167987, \"Recovered/100k\": 0.0, \"Confirmed\": 137.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": -80.11915156, \"Lat\": 8.51750797}, {\"Country/Region\": \"Peru\", \"Confirmed/100k\": 0.7314955996475817, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0031260495711435115, \"Confirmed\": 234.0, \"Deaths\": 3.0, \"Recovered\": 1.0, \"Long\": -74.38242685, \"Lat\": -9.15280381}, {\"Country/Region\": \"Philippines\", \"Confirmed/100k\": 0.2034656253077183, \"Deaths/100k\": 0.01593970336512079, \"Recovered/100k\": 0.007501036877703902, \"Confirmed\": 230.0, \"Deaths\": 18.0, \"Recovered\": 8.0, \"Long\": 122.88393253, \"Lat\": 11.77536778}, {\"Country/Region\": \"Poland\", \"Confirmed/100k\": 0.9347382106340664, \"Deaths/100k\": 0.013165326910338962, \"Recovered/100k\": 0.002633065382067793, \"Confirmed\": 425.0, \"Deaths\": 5.0, \"Recovered\": 1.0, \"Long\": 19.39012835, \"Lat\": 52.12759564}, {\"Country/Region\": \"Portugal\", \"Confirmed/100k\": 7.634878146372187, \"Deaths/100k\": 0.029177878266390532, \"Recovered/100k\": 0.029177878266390532, \"Confirmed\": 1020.0, \"Deaths\": 6.0, \"Recovered\": 5.0, \"Long\": -8.50104361, \"Lat\": 39.59550671}, {\"Country/Region\": \"Qatar\", \"Confirmed/100k\": 16.536786981378498, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.14379814766416085, \"Confirmed\": 470.0, \"Deaths\": 0.0, \"Recovered\": 10.0, \"Long\": 51.18479632, \"Lat\": 25.30601188}, {\"Country/Region\": \"Romania\", \"Confirmed/100k\": 1.4224140410033186, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.12837671850210455, \"Confirmed\": 308.0, \"Deaths\": 0.0, \"Recovered\": 25.0, \"Long\": 24.97293039, \"Lat\": 45.85243127}, {\"Country/Region\": \"Russia\", \"Confirmed/100k\": 0.13773718568322316, \"Deaths/100k\": 0.0006921466617247395, \"Recovered/100k\": 0.006229319955522656, \"Confirmed\": 253.0, \"Deaths\": 1.0, \"Recovered\": 9.0, \"Long\": 96.68656112, \"Lat\": 61.98052209}, {\"Country/Region\": \"Saudi Arabia\", \"Confirmed/100k\": 0.8130576585179794, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.01780418230331341, \"Confirmed\": 344.0, \"Deaths\": 0.0, \"Recovered\": 8.0, \"Long\": 44.53686271, \"Lat\": 24.12245841}, {\"Country/Region\": \"Serbia\", \"Confirmed/100k\": 1.4752042513381391, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.014322371372214943, \"Confirmed\": 135.0, \"Deaths\": 1.0, \"Recovered\": 1.0, \"Long\": 20.78958334, \"Lat\": 44.2215032}, {\"Country/Region\": \"Singapore\", \"Confirmed/100k\": 6.118457595364586, \"Deaths/100k\": 0.0, \"Recovered/100k\": 2.0217512054248195, \"Confirmed\": 385.0, \"Deaths\": 0.0, \"Recovered\": 124.0, \"Long\": 103.81725592, \"Lat\": 1.35876087}, {\"Country/Region\": \"Slovakia\", \"Confirmed/100k\": 2.258119177655415, \"Deaths/100k\": 0.018358692501263537, \"Recovered/100k\": 0.0, \"Confirmed\": 137.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 19.47905218, \"Lat\": 48.70547528}, {\"Country/Region\": \"Slovenia\", \"Confirmed/100k\": 13.833988271099733, \"Deaths/100k\": 0.04837058836048858, \"Recovered/100k\": 0.0, \"Confirmed\": 341.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 14.80444238, \"Lat\": 46.11554772}, {\"Country/Region\": \"South Africa\", \"Confirmed/100k\": 0.25960709815650923, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 202.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 25.08390093, \"Lat\": -29.00034095}, {\"Country/Region\": \"Spain\", \"Confirmed/100k\": 38.445117064557465, \"Deaths/100k\": 1.7763985505529534, \"Recovered/100k\": 2.3692448138097824, \"Confirmed\": 20410.0, \"Deaths\": 1043.0, \"Recovered\": 1588.0, \"Long\": -3.64755047, \"Lat\": 40.24448698}, {\"Country/Region\": \"Sweden\", \"Confirmed/100k\": 14.131152612029155, \"Deaths/100k\": 0.10802131948041746, \"Recovered/100k\": 0.15712191924424354, \"Confirmed\": 1639.0, \"Deaths\": 16.0, \"Recovered\": 16.0, \"Long\": 16.74558049, \"Lat\": 62.77966519}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 47.84805290127696, \"Deaths/100k\": 0.4814159923809461, \"Recovered/100k\": 0.17612780209059006, \"Confirmed\": 5294.0, \"Deaths\": 54.0, \"Recovered\": 15.0, \"Long\": 8.20867471, \"Lat\": 46.79785878}, {\"Country/Region\": \"Taiwan*\", \"Confirmed/100k\": 0.4700895307274674, \"Deaths/100k\": 0.004352680840069143, \"Recovered/100k\": 0.11316970184179773, \"Confirmed\": 135.0, \"Deaths\": 2.0, \"Recovered\": 26.0, \"Long\": 120.95427281, \"Lat\": 23.7539928}, {\"Country/Region\": \"Thailand\", \"Confirmed/100k\": 0.3917698149538653, \"Deaths/100k\": 0.0014403302020362695, \"Recovered/100k\": 0.06049386848552332, \"Confirmed\": 322.0, \"Deaths\": 1.0, \"Recovered\": 42.0, \"Long\": 101.0028813, \"Lat\": 15.11815794}, {\"Country/Region\": \"Turkey\", \"Confirmed/100k\": 0.2332369335932176, \"Deaths/100k\": 0.003644327087394025, \"Recovered/100k\": 0.0, \"Confirmed\": 359.0, \"Deaths\": 4.0, \"Recovered\": 0.0, \"Long\": 35.16895346, \"Lat\": 39.0616029}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 4.1804283002078995, \"Deaths/100k\": 0.06113077868257511, \"Recovered/100k\": 0.0, \"Confirmed\": 19100.0, \"Deaths\": 244.0, \"Recovered\": 0.0, \"Long\": -112.4616737, \"Lat\": 45.6795472}, {\"Country/Region\": \"United Arab Emirates\", \"Confirmed/100k\": 1.4536454780879038, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.3218786415766073, \"Confirmed\": 140.0, \"Deaths\": 2.0, \"Recovered\": 31.0, \"Long\": 54.3001671, \"Lat\": 23.90528188}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 4.084886774714328, \"Deaths/100k\": 0.20755315718357045, \"Recovered/100k\": 0.10076856182100884, \"Confirmed\": 4014.0, \"Deaths\": 178.0, \"Recovered\": 67.0, \"Long\": -2.86563164, \"Lat\": 54.12387156}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.LayerChart(...)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
       "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
       "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
       "</p>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "display(helper.map_of_variable(map_df, 'Confirmed/100k', 'Confirmed'))\n",
    "display(HTML('''\n",
    "<p style=\"font-size: smaller\">Data Sources: \n",
    "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
    "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
    "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
    "</p>'''))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "papermill": {
     "duration": 0.121229,
     "end_time": "2020-03-21T08:21:35.733198",
     "exception": false,
     "start_time": "2020-03-21T08:21:35.611969",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<div id=\"altair-viz-1ee73cb55d3a4a61aed54cbd6a511d94\"></div>\n",
       "<script type=\"text/javascript\">\n",
       "  (function(spec, embedOpt){\n",
       "    const outputDiv = document.getElementById(\"altair-viz-1ee73cb55d3a4a61aed54cbd6a511d94\");\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\": [{\"mark\": \"bar\", \"encoding\": {\"tooltip\": [{\"type\": \"nominal\", \"field\": \"Country/Region\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed\"}, {\"type\": \"quantitative\", \"field\": \"Deaths\"}, {\"type\": \"quantitative\", \"field\": \"Recovered\"}, {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, {\"type\": \"quantitative\", \"field\": \"Deaths/100k\"}, {\"type\": \"quantitative\", \"field\": \"Recovered/100k\"}], \"x\": {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\"}, \"y\": {\"type\": \"nominal\", \"field\": \"Country/Region\", \"sort\": \"-x\"}}}, {\"mark\": {\"type\": \"text\", \"align\": \"left\", \"baseline\": \"middle\", \"dx\": 3}, \"encoding\": {\"text\": {\"type\": \"quantitative\", \"field\": \"Confirmed/100k\", \"format\": \".3\"}, \"tooltip\": [{\"type\": \"nominal\", \"field\": \"Country/Region\"}, {\"type\": 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-35.3813488}, {\"Country/Region\": \"Armenia\", \"Confirmed/100k\": 3.895959585009161, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.03387790943486227, \"Confirmed\": 136.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 44.92993276, \"Lat\": 40.28952569}, {\"Country/Region\": \"Australia\", \"Confirmed/100k\": 2.724831727636544, \"Deaths/100k\": 0.024007327996797743, \"Recovered/100k\": 0.1040317546527902, \"Confirmed\": 791.0, \"Deaths\": 7.0, \"Recovered\": 26.0, \"Long\": 134.49100008, \"Lat\": -25.73288704}, {\"Country/Region\": \"Austria\", \"Confirmed/100k\": 22.753380595107718, \"Deaths/100k\": 0.06781931622982926, \"Recovered/100k\": 0.1017289743447439, \"Confirmed\": 2388.0, \"Deaths\": 6.0, \"Recovered\": 9.0, \"Long\": 14.1264761, \"Lat\": 47.58549439}, {\"Country/Region\": \"Bahrain\", \"Confirmed/100k\": 17.713335784315287, \"Deaths/100k\": 0.06371703519537872, \"Recovered/100k\": 6.371703519537872, \"Confirmed\": 285.0, \"Deaths\": 1.0, \"Recovered\": 100.0, \"Long\": 50.54196932, \"Lat\": 26.04205135}, {\"Country/Region\": \"Belgium\", \"Confirmed/100k\": 15.715192730423247, \"Deaths/100k\": 0.1838546224729182, \"Recovered/100k\": 0.27140444269811737, \"Confirmed\": 2257.0, \"Deaths\": 37.0, \"Recovered\": 1.0, \"Long\": 4.64065114, \"Lat\": 50.63981576}, {\"Country/Region\": \"Brazil\", \"Confirmed/100k\": 0.29646344460360696, \"Deaths/100k\": 0.0028643811072812265, \"Recovered/100k\": 0.0009547937024270756, \"Confirmed\": 793.0, \"Deaths\": 11.0, \"Recovered\": 2.0, \"Long\": -53.09783113, \"Lat\": -10.78777702}, {\"Country/Region\": \"Bulgaria\", \"Confirmed/100k\": 1.3382276399245123, \"Deaths/100k\": 0.04270939276354828, \"Recovered/100k\": 0.0, \"Confirmed\": 127.0, \"Deaths\": 3.0, \"Recovered\": 0.0, \"Long\": 25.21552909, \"Lat\": 42.76890318}, {\"Country/Region\": \"Canada\", \"Confirmed/100k\": 2.1587282672730104, \"Deaths/100k\": 0.02428569300682137, \"Recovered/100k\": 0.02428569300682137, \"Confirmed\": 943.0, \"Deaths\": 12.0, \"Recovered\": 9.0, \"Long\": -98.30777028, \"Lat\": 61.36206324}, {\"Country/Region\": \"Chile\", \"Confirmed/100k\": 1.2707457248483114, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 434.0, \"Deaths\": 0.0, \"Recovered\": 6.0, \"Long\": -71.38256213, \"Lat\": -37.73070989}, {\"Country/Region\": \"China\", \"Confirmed/100k\": 5.827116526534216, \"Deaths/100k\": 0.2332828329970633, \"Recovered/100k\": 5.064513581239722, \"Confirmed\": 81250.0, \"Deaths\": 3253.0, \"Recovered\": 71266.0, \"Long\": 103.81907349, \"Lat\": 36.56176546}, {\"Country/Region\": \"Colombia\", \"Confirmed/100k\": 0.20544350771828093, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.002014152036453735, \"Confirmed\": 128.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": -73.08114582, \"Lat\": 3.91383431}, {\"Country/Region\": \"Croatia\", \"Confirmed/100k\": 2.567613830879836, \"Deaths/100k\": 0.02445346505599844, \"Recovered/100k\": 0.12226732527999218, \"Confirmed\": 128.0, \"Deaths\": 1.0, \"Recovered\": 5.0, \"Long\": 16.40412899, \"Lat\": 45.08047631}, {\"Country/Region\": \"Czechia\", \"Confirmed/100k\": 6.531337479571924, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.028233447318034257, \"Confirmed\": 833.0, \"Deaths\": 0.0, \"Recovered\": 4.0, \"Long\": 15.31240163, \"Lat\": 49.73341233}, {\"Country/Region\": \"Denmark\", \"Confirmed/100k\": 21.12999413879836, \"Deaths/100k\": 0.10349384884309402, \"Recovered/100k\": 0.01724897480718234, \"Confirmed\": 1337.0, \"Deaths\": 9.0, \"Recovered\": 1.0, \"Long\": 10.02800992, \"Lat\": 55.98125296}, {\"Country/Region\": \"Ecuador\", \"Confirmed/100k\": 1.1648082511972797, \"Deaths/100k\": 0.01755992338488361, \"Recovered/100k\": 0.0, \"Confirmed\": 367.0, \"Deaths\": 5.0, \"Recovered\": 0.0, \"Long\": -78.75201922, \"Lat\": -1.42381612}, {\"Country/Region\": \"Egypt\", \"Confirmed/100k\": 0.2601002330792733, \"Deaths/100k\": 0.0060960992127954685, \"Recovered/100k\": 0.032512529134909166, \"Confirmed\": 285.0, \"Deaths\": 8.0, \"Recovered\": 39.0, \"Long\": 29.86190099, \"Lat\": 26.49593311}, {\"Country/Region\": \"Estonia\", \"Confirmed/100k\": 20.213735649761826, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.07570687509274092, \"Confirmed\": 283.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 25.54248537, \"Lat\": 58.67192972}, {\"Country/Region\": \"Finland\", \"Confirmed/100k\": 7.248937577586285, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.18122343943965716, \"Confirmed\": 450.0, \"Deaths\": 0.0, \"Recovered\": 10.0, \"Long\": 26.2746656, \"Lat\": 64.49884603}, {\"Country/Region\": \"France\", \"Confirmed/100k\": 16.341917276071243, \"Deaths/100k\": 0.3627556315050071, \"Recovered/100k\": 0.017913858345926282, \"Confirmed\": 12726.0, \"Deaths\": 450.0, \"Recovered\": 12.0, \"Long\": -2.76172945, \"Lat\": 42.17344011}, {\"Country/Region\": \"Germany\", \"Confirmed/100k\": 18.473874215731584, \"Deaths/100k\": 0.05305812437938575, \"Recovered/100k\": 0.13626291033796795, \"Confirmed\": 19848.0, \"Deaths\": 67.0, \"Recovered\": 180.0, \"Long\": 10.38578051, \"Lat\": 51.10698181}, {\"Country/Region\": \"Greece\", \"Confirmed/100k\": 3.896466594603785, \"Deaths/100k\": 0.055930142506274434, \"Recovered/100k\": 0.07457352334169924, \"Confirmed\": 495.0, \"Deaths\": 6.0, \"Recovered\": 19.0, \"Long\": 22.95555794, \"Lat\": 39.07469623}, {\"Country/Region\": \"India\", \"Confirmed/100k\": 0.01434256356059339, \"Deaths/100k\": 0.00029572296001223485, \"Recovered/100k\": 0.0011089611000458808, \"Confirmed\": 244.0, \"Deaths\": 5.0, \"Recovered\": 20.0, \"Long\": 79.61197609999998, \"Lat\": 22.88578212}, {\"Country/Region\": \"Indonesia\", \"Confirmed/100k\": 0.11619069298725845, \"Deaths/100k\": 0.009340087860712092, \"Recovered/100k\": 0.004109638658713321, \"Confirmed\": 369.0, \"Deaths\": 32.0, \"Recovered\": 15.0, \"Long\": 117.24011366, \"Lat\": -2.21505456}, {\"Country/Region\": \"Iran\", \"Confirmed/100k\": 22.5023709885355, \"Deaths/100k\": 1.569676989693029, \"Recovered/100k\": 6.980417142638004, \"Confirmed\": 19644.0, \"Deaths\": 1433.0, \"Recovered\": 6745.0, \"Long\": 54.27407004, \"Lat\": 32.57503292}, {\"Country/Region\": \"Iraq\", \"Confirmed/100k\": 0.4995628824778319, \"Deaths/100k\": 0.033824570167769866, \"Recovered/100k\": 0.1118812705549311, \"Confirmed\": 208.0, \"Deaths\": 17.0, \"Recovered\": 49.0, \"Long\": 43.74353149, \"Lat\": 33.03970582}, {\"Country/Region\": \"Ireland\", \"Confirmed/100k\": 11.47624006233844, \"Deaths/100k\": 0.06181098776842967, \"Recovered/100k\": 0.10301831294738276, \"Confirmed\": 683.0, \"Deaths\": 3.0, \"Recovered\": 5.0, \"Long\": -8.13793569, \"Lat\": 53.17544870000001}, {\"Country/Region\": \"Israel\", \"Confirmed/100k\": 7.620612800828473, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.12382088745806975, \"Confirmed\": 705.0, \"Deaths\": 0.0, \"Recovered\": 14.0, \"Long\": 35.00444693, \"Lat\": 31.46110101}, {\"Country/Region\": \"Italy\", \"Confirmed/100k\": 67.90357239312625, \"Deaths/100k\": 5.634498939895088, \"Recovered/100k\": 7.347188044973329, \"Confirmed\": 47021.0, \"Deaths\": 4032.0, \"Recovered\": 4440.0, \"Long\": 12.07001339, \"Lat\": 42.79662641}, {\"Country/Region\": \"Japan\", \"Confirmed/100k\": 0.7302667923821476, \"Deaths/100k\": 0.02291962876524057, \"Recovered/100k\": 0.11854980395814085, \"Confirmed\": 963.0, \"Deaths\": 33.0, \"Recovered\": 191.0, \"Long\": 138.03089558, \"Lat\": 37.59230135}, {\"Country/Region\": \"Korea, South\", \"Confirmed/100k\": 16.58750370095967, \"Deaths/100k\": 0.1762361747562557, \"Recovered/100k\": 2.9824583420289423, \"Confirmed\": 8652.0, \"Deaths\": 94.0, \"Recovered\": 1540.0, \"Long\": 127.83916086, \"Lat\": 36.38523983}, {\"Country/Region\": \"Kuwait\", \"Confirmed/100k\": 3.577204409919588, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.4350654012064364, \"Confirmed\": 159.0, \"Deaths\": 0.0, \"Recovered\": 18.0, \"Long\": 47.58700459, \"Lat\": 29.33431262}, {\"Country/Region\": \"Latvia\", \"Confirmed/100k\": 4.4639566643239545, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.05190647284097621, \"Confirmed\": 111.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 24.91235983, \"Lat\": 56.85085163}, {\"Country/Region\": \"Lebanon\", \"Confirmed/100k\": 2.2923305482247214, \"Deaths/100k\": 0.05840332606941965, \"Recovered/100k\": 0.05840332606941965, \"Confirmed\": 163.0, \"Deaths\": 4.0, \"Recovered\": 4.0, \"Long\": 35.88016072, \"Lat\": 33.92306631}, {\"Country/Region\": \"Luxembourg\", \"Confirmed/100k\": 55.123344654187406, \"Deaths/100k\": 0.658189189900745, \"Recovered/100k\": 0.0, \"Confirmed\": 484.0, \"Deaths\": 4.0, \"Recovered\": 0.0, \"Long\": 6.07182201, \"Lat\": 49.76725361}, {\"Country/Region\": \"Malaysia\", \"Confirmed/100k\": 2.8545524640576163, \"Deaths/100k\": 0.0063434499201280355, \"Recovered/100k\": 0.23787937200480136, \"Confirmed\": 1030.0, \"Deaths\": 3.0, \"Recovered\": 87.0, \"Long\": 109.69762284, \"Lat\": 3.78986846}, {\"Country/Region\": \"Mexico\", \"Confirmed/100k\": 0.09350920290631674, \"Deaths/100k\": 0.0007924508720874299, \"Recovered/100k\": 0.0031698034883497197, \"Confirmed\": 164.0, \"Deaths\": 1.0, \"Recovered\": 4.0, \"Long\": -102.52345169, \"Lat\": 23.94753724}, {\"Country/Region\": \"Netherlands\", \"Confirmed/100k\": 14.317204840550039, \"Deaths/100k\": 0.4468685742692959, \"Recovered/100k\": 0.011606975955046644, \"Confirmed\": 3003.0, \"Deaths\": 107.0, \"Recovered\": 2.0, \"Long\": 5.28144793, \"Lat\": 52.1007899}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 32.85452782812378, \"Deaths/100k\": 0.131719183732455, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 1914.0, \"Deaths\": 7.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572}, {\"Country/Region\": \"Pakistan\", \"Confirmed/100k\": 0.213933951803508, \"Deaths/100k\": 0.0009424403163150133, \"Recovered/100k\": 0.006125862056047585, \"Confirmed\": 501.0, \"Deaths\": 3.0, \"Recovered\": 13.0, \"Long\": 69.33957937, \"Lat\": 29.9497515}, {\"Country/Region\": \"Panama\", \"Confirmed/100k\": 2.609607713713105, \"Deaths/100k\": 0.02394135517167987, \"Recovered/100k\": 0.0, \"Confirmed\": 137.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": -80.11915156, \"Lat\": 8.51750797}, {\"Country/Region\": \"Peru\", \"Confirmed/100k\": 0.7314955996475817, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0031260495711435115, \"Confirmed\": 234.0, \"Deaths\": 3.0, \"Recovered\": 1.0, \"Long\": -74.38242685, \"Lat\": -9.15280381}, {\"Country/Region\": \"Philippines\", \"Confirmed/100k\": 0.2034656253077183, \"Deaths/100k\": 0.01593970336512079, \"Recovered/100k\": 0.007501036877703902, \"Confirmed\": 230.0, \"Deaths\": 18.0, \"Recovered\": 8.0, \"Long\": 122.88393253, \"Lat\": 11.77536778}, {\"Country/Region\": \"Poland\", \"Confirmed/100k\": 0.9347382106340664, \"Deaths/100k\": 0.013165326910338962, \"Recovered/100k\": 0.002633065382067793, \"Confirmed\": 425.0, \"Deaths\": 5.0, \"Recovered\": 1.0, \"Long\": 19.39012835, \"Lat\": 52.12759564}, {\"Country/Region\": \"Portugal\", \"Confirmed/100k\": 7.634878146372187, \"Deaths/100k\": 0.029177878266390532, \"Recovered/100k\": 0.029177878266390532, \"Confirmed\": 1020.0, \"Deaths\": 6.0, \"Recovered\": 5.0, \"Long\": -8.50104361, \"Lat\": 39.59550671}, {\"Country/Region\": \"Qatar\", \"Confirmed/100k\": 16.536786981378498, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.14379814766416085, \"Confirmed\": 470.0, \"Deaths\": 0.0, \"Recovered\": 10.0, \"Long\": 51.18479632, \"Lat\": 25.30601188}, {\"Country/Region\": \"Romania\", \"Confirmed/100k\": 1.4224140410033186, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.12837671850210455, \"Confirmed\": 308.0, \"Deaths\": 0.0, \"Recovered\": 25.0, \"Long\": 24.97293039, \"Lat\": 45.85243127}, {\"Country/Region\": \"Russia\", \"Confirmed/100k\": 0.13773718568322316, \"Deaths/100k\": 0.0006921466617247395, \"Recovered/100k\": 0.006229319955522656, \"Confirmed\": 253.0, \"Deaths\": 1.0, \"Recovered\": 9.0, \"Long\": 96.68656112, \"Lat\": 61.98052209}, {\"Country/Region\": \"Saudi Arabia\", \"Confirmed/100k\": 0.8130576585179794, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.01780418230331341, \"Confirmed\": 344.0, \"Deaths\": 0.0, \"Recovered\": 8.0, \"Long\": 44.53686271, \"Lat\": 24.12245841}, {\"Country/Region\": \"Serbia\", \"Confirmed/100k\": 1.4752042513381391, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.014322371372214943, \"Confirmed\": 135.0, \"Deaths\": 1.0, \"Recovered\": 1.0, \"Long\": 20.78958334, \"Lat\": 44.2215032}, {\"Country/Region\": \"Singapore\", \"Confirmed/100k\": 6.118457595364586, \"Deaths/100k\": 0.0, \"Recovered/100k\": 2.0217512054248195, \"Confirmed\": 385.0, \"Deaths\": 0.0, \"Recovered\": 124.0, \"Long\": 103.81725592, \"Lat\": 1.35876087}, {\"Country/Region\": \"Slovakia\", \"Confirmed/100k\": 2.258119177655415, \"Deaths/100k\": 0.018358692501263537, \"Recovered/100k\": 0.0, \"Confirmed\": 137.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 19.47905218, \"Lat\": 48.70547528}, {\"Country/Region\": \"Slovenia\", \"Confirmed/100k\": 13.833988271099733, \"Deaths/100k\": 0.04837058836048858, \"Recovered/100k\": 0.0, \"Confirmed\": 341.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 14.80444238, \"Lat\": 46.11554772}, {\"Country/Region\": \"South Africa\", \"Confirmed/100k\": 0.25960709815650923, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 202.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 25.08390093, \"Lat\": -29.00034095}, {\"Country/Region\": \"Spain\", \"Confirmed/100k\": 38.445117064557465, \"Deaths/100k\": 1.7763985505529534, \"Recovered/100k\": 2.3692448138097824, \"Confirmed\": 20410.0, \"Deaths\": 1043.0, \"Recovered\": 1588.0, \"Long\": -3.64755047, \"Lat\": 40.24448698}, {\"Country/Region\": \"Sweden\", \"Confirmed/100k\": 14.131152612029155, \"Deaths/100k\": 0.10802131948041746, \"Recovered/100k\": 0.15712191924424354, \"Confirmed\": 1639.0, \"Deaths\": 16.0, \"Recovered\": 16.0, \"Long\": 16.74558049, \"Lat\": 62.77966519}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 47.84805290127696, \"Deaths/100k\": 0.4814159923809461, \"Recovered/100k\": 0.17612780209059006, \"Confirmed\": 5294.0, \"Deaths\": 54.0, \"Recovered\": 15.0, \"Long\": 8.20867471, \"Lat\": 46.79785878}, {\"Country/Region\": \"Taiwan*\", \"Confirmed/100k\": 0.4700895307274674, \"Deaths/100k\": 0.004352680840069143, \"Recovered/100k\": 0.11316970184179773, \"Confirmed\": 135.0, \"Deaths\": 2.0, \"Recovered\": 26.0, \"Long\": 120.95427281, \"Lat\": 23.7539928}, {\"Country/Region\": \"Thailand\", \"Confirmed/100k\": 0.3917698149538653, \"Deaths/100k\": 0.0014403302020362695, \"Recovered/100k\": 0.06049386848552332, \"Confirmed\": 322.0, \"Deaths\": 1.0, \"Recovered\": 42.0, \"Long\": 101.0028813, \"Lat\": 15.11815794}, {\"Country/Region\": \"Turkey\", \"Confirmed/100k\": 0.2332369335932176, \"Deaths/100k\": 0.003644327087394025, \"Recovered/100k\": 0.0, \"Confirmed\": 359.0, \"Deaths\": 4.0, \"Recovered\": 0.0, \"Long\": 35.16895346, \"Lat\": 39.0616029}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 4.1804283002078995, \"Deaths/100k\": 0.06113077868257511, \"Recovered/100k\": 0.0, \"Confirmed\": 19100.0, \"Deaths\": 244.0, \"Recovered\": 0.0, \"Long\": -112.4616737, \"Lat\": 45.6795472}, {\"Country/Region\": \"United Arab Emirates\", \"Confirmed/100k\": 1.4536454780879038, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.3218786415766073, \"Confirmed\": 140.0, \"Deaths\": 2.0, \"Recovered\": 31.0, \"Long\": 54.3001671, \"Lat\": 23.90528188}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 4.084886774714328, \"Deaths/100k\": 0.20755315718357045, \"Recovered/100k\": 0.10076856182100884, \"Confirmed\": 4014.0, \"Deaths\": 178.0, \"Recovered\": 67.0, \"Long\": -2.86563164, \"Lat\": 54.12387156}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.LayerChart(...)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
       "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
       "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
       "</p>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "bars = alt.Chart(map_df).mark_bar().encode(\n",
    "    x='Confirmed/100k:Q',\n",
    "    y=alt.Y(\"Country/Region:N\", sort='-x'),\n",
    "    tooltip=[\"Country/Region:N\", \n",
    "         \"Confirmed:Q\", \"Deaths:Q\", \"Recovered:Q\",\n",
    "         \"Confirmed/100k:Q\", \"Deaths/100k:Q\", \"Recovered/100k:Q\"]\n",
    ")\n",
    "\n",
    "text = bars.mark_text(\n",
    "    align='left',\n",
    "    baseline='middle',\n",
    "    dx=3  # Nudges text to right so it doesn't appear on top of the bar\n",
    ").encode(\n",
    "    text=alt.Text('Confirmed/100k:Q', format=\".3\")\n",
    ")\n",
    "\n",
    "chart = (bars + text).properties(height=900, title=f\"Confirmed cases per 100k inhabitants\")\n",
    "display(chart)\n",
    "display(HTML('''\n",
    "<p style=\"font-size: smaller\">Data Sources: \n",
    "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
    "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
    "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
    "</p>'''))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "papermill": {
     "duration": 0.016329,
     "end_time": "2020-03-21T08:21:35.766114",
     "exception": false,
     "start_time": "2020-03-21T08:21:35.749785",
     "status": "completed"
    },
    "tags": []
   },
   "source": [
    "## How have cases been growing?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "papermill": {
     "duration": 0.085944,
     "end_time": "2020-03-21T08:21:35.868183",
     "exception": false,
     "start_time": "2020-03-21T08:21:35.782239",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "confirmed_rate_df = helper.growth_df(rates_frames_map, geodata_df, 'confirmed', countries_over_thresh, 2)\n",
    "latest_confirmed_ser = confirmed_rate_df.set_index(\n",
    "    ['Country/Region', 'Geo Region', 'Date']).drop(\n",
    "    ['Longitude', 'Latitude'], axis=1).unstack().iloc[:,-1]\n",
    "sort_order = latest_confirmed_ser.groupby('Geo Region').mean().sort_values(ascending=False).index.tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
    "papermill": {
     "duration": 0.167666,
     "end_time": "2020-03-21T08:21:36.055819",
     "exception": false,
     "start_time": "2020-03-21T08:21:35.888153",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "    const outputDiv = document.getElementById(\"altair-viz-d35a7707f871457484f71238619832d4\");\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",
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       "    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",
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\"Europe\", \"Date\": \"2020-02-10T00:00:00\", \"Confirmed/100k\": 0.012032067083105532}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-11T00:00:00\", \"Confirmed/100k\": 0.012032067083105532}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-12T00:00:00\", \"Confirmed/100k\": 0.013536075468493723}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-13T00:00:00\", \"Confirmed/100k\": 0.013536075468493723}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-14T00:00:00\", \"Confirmed/100k\": 0.013536075468493723}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo 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\"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-25T00:00:00\", \"Confirmed/100k\": 0.01955210901004649}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-26T00:00:00\", \"Confirmed/100k\": 0.01955210901004649}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-27T00:00:00\", \"Confirmed/100k\": 0.022560125780822875}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-28T00:00:00\", \"Confirmed/100k\": 0.030080167707763825}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-29T00:00:00\", \"Confirmed/100k\": 0.034592192863928416}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": 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\"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-11T00:00:00\", \"Confirmed/100k\": 0.6903398488931799}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-12T00:00:00\", \"Confirmed/100k\": 0.6903398488931799}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-13T00:00:00\", \"Confirmed/100k\": 1.2062147250813295}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-14T00:00:00\", \"Confirmed/100k\": 1.7205855928840912}, {\"Country/Region\": \"United Kingdom\", \"Longitude\": -2.86563164, \"Latitude\": 54.12387156, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-15T00:00:00\", \"Confirmed/100k\": 1.7220896012694793}, {\"Country/Region\": \"United Kingdom\", 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       "</script>"
      ],
      "text/plain": [
       "alt.Chart(...)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
       "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
       "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
       "</p>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
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   ],
   "source": [
    "base = alt.Chart(confirmed_rate_df).properties(\n",
    "    width=300, height=200, title=\"Countries with 2 or more cases per 100k\")\n",
    "line = base.mark_line().encode(\n",
    "    x='Date',\n",
    "    y='Confirmed/100k',\n",
    "    color='Country/Region',\n",
    "    facet=alt.Facet('Geo Region:N', columns=1, sort=alt.SortArray(sort_order), title='Geographic Region'),\n",
    "    tooltip=[\"Country/Region:N\", \"Date:T\", \"Confirmed/100k:Q\"]\n",
    ")\n",
    "line\n",
    "display(line)\n",
    "display(HTML('''\n",
    "<p style=\"font-size: smaller\">Data Sources: \n",
    "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
    "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
    "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
    "</p>'''))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "papermill": {
     "duration": 0.365646,
     "end_time": "2020-03-21T08:21:36.447346",
     "exception": false,
     "start_time": "2020-03-21T08:21:36.081700",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "def country_increase_df(c, df_nominal, growth_in_rate_df):\n",
    "    over_100 = df_nominal[df_nominal['Confirmed'] >= 100]\n",
    "    tdf = (over_100[['Date', 'Confirmed']] - over_100.iloc[0][['Date', 'Confirmed']]).reset_index()\n",
    "    tdfr = growth_in_rate_df[(growth_in_rate_df['Date'] >= over_100.iloc[0]['Date']) &\n",
    "                             (growth_in_rate_df['Country/Region'] == c)].reset_index()\n",
    "    tdf['Confirmed/100k'] = tdfr['Confirmed/100k']\n",
    "    tdf['Country/Region'] = c\n",
    "    tdf['Days'] = (tdf['Date'] / np.timedelta64(1, 'D')).astype(int)\n",
    "    return tdf[['Country/Region', 'Days', 'Confirmed', 'Confirmed/100k']]\n",
    "\n",
    "\n",
    "growth_in_rate_df = helper.growth_df(rates_frames_map, geodata_df, 'confirmed', countries_over_thresh, 0)\n",
    "frame_map = {'confirmed': jhu_frames_map['confirmed'].groupby(level='Country/Region').sum()}\n",
    "growth_in_value_df = helper.growth_df(frame_map, geodata_df, 'confirmed', countries_over_thresh, 1000)\n",
    "growth_in_value_df = growth_in_value_df.rename({'Confirmed/100k':'Confirmed'}, axis=1)\n",
    "increase_df = pd.concat([country_increase_df(c, df_nominal, growth_in_rate_df) for \n",
    "                         c, df_nominal in growth_in_value_df.groupby('Country/Region')])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "papermill": {
     "duration": 0.046133,
     "end_time": "2020-03-21T08:21:36.524965",
     "exception": false,
     "start_time": "2020-03-21T08:21:36.478832",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "def facetted_growth_plot(df, variable, sort_order, ref_country, title, yscale='linear'):\n",
    "    base = alt.Chart(df).properties(\n",
    "        width=250, height=150)\n",
    "    line = base.mark_line().encode(\n",
    "        x='Days',\n",
    "        y=variable,\n",
    "        color='Country/Region',\n",
    "        tooltip=[\"Country/Region:N\", \"Days:Q\", f\"{variable}:Q\"]\n",
    "    )\n",
    "    label_loc = increase_df[increase_df['Country/Region'] == ref_country]['Days'].iloc[-2]\n",
    "    ref = base.mark_line(opacity=0.3).encode(\n",
    "        x='Days',\n",
    "        y=alt.Y(variable, scale=alt.Scale(type=yscale)),\n",
    "        color=alt.ColorValue('steelblue'),\n",
    "    ).transform_filter(f\"datum['Country/Region'] == '{ref_country}'\")\n",
    "    ref += ref.mark_text().encode(text='Country/Region:N').transform_filter(f\"datum['Days'] == {label_loc}\")\n",
    "    charts = []\n",
    "    # make our small multiples\n",
    "    for country in sort_order:\n",
    "        smallm = line.transform_filter(f\"datum['Country/Region'] == '{country}'\").properties(\n",
    "            title=country)\n",
    "        smallm += ref\n",
    "        charts.append(smallm)\n",
    "\n",
    "    # group the small multiples into 3 horizontal charts\n",
    "    groups = []\n",
    "    c = None\n",
    "    for i, chart in enumerate(charts):\n",
    "        if not i%3:\n",
    "            if c != None:\n",
    "                groups.append(c)\n",
    "            c = alt.hconcat()\n",
    "        c |= chart\n",
    "    # vertically combine the horizontal charts\n",
    "    chart = alt.vconcat(title=title)\n",
    "    for c in groups:\n",
    "        chart &= c\n",
    "    return chart"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "papermill": {
     "duration": 0.381155,
     "end_time": "2020-03-21T08:21:36.935070",
     "exception": false,
     "start_time": "2020-03-21T08:21:36.553915",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
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       "  (function(spec, embedOpt){\n",
       "    const outputDiv = document.getElementById(\"altair-viz-759454c2bc714c72a9efb1b63c824f68\");\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",
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       "\n",
       "    function loadScript(lib) {\n",
       "      return new Promise(function(resolve, reject) {\n",
       "        var s = document.createElement('script');\n",
       "        s.src = paths[lib];\n",
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       "        s.onload = () => resolve(paths[lib]);\n",
       "        s.onerror = () => reject(`Error loading script: ${paths[lib]}`);\n",
       "        document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
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       "\n",
       "    function showError(err) {\n",
       "      outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
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       "    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",
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       "      loadScript(\"vega\")\n",
       "        .then(() => loadScript(\"vega-lite\"))\n",
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{\"Country/Region\": \"United Kingdom\", \"Days\": 14, \"Confirmed\": 2600, \"Confirmed/100k\": 4.084886774714328}, {\"Country/Region\": \"United Kingdom\", \"Days\": 15, \"Confirmed\": 3898, \"Confirmed/100k\": null}]}}, {\"mode\": \"vega-lite\"});\n",
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       "alt.VConcatChart(...)"
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       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
       "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
       "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
       "</p>\n",
       "<p style=\"font-size: smaller\">Inspired by <a href=\"https://covid19dashboards.com/growth-analysis/\">Thomas Wiecki</a>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
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   "source": [
    "sort_order = growth_in_value_df.groupby(\n",
    "    'Country/Region').max().sort_values(\n",
    "    'Confirmed', ascending=False).index.tolist()\n",
    "# Exclude China in this plot because its numbers are far greater then everywhere else\n",
    "sort_order = [o for o in sort_order if o != 'China']\n",
    "chart = facetted_growth_plot(increase_df[increase_df['Country/Region'] != 'China'], \n",
    "                             'Confirmed',\n",
    "                             sort_order,\n",
    "                             'Italy',\n",
    "                             \"Growth of cases from case 100, compared to Italy\")\n",
    "display(chart)\n",
    "display(HTML('''\n",
    "<p style=\"font-size: smaller\">Data Sources: \n",
    "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
    "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
    "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
    "</p>\n",
    "<p style=\"font-size: smaller\">Inspired by <a href=\"https://covid19dashboards.com/growth-analysis/\">Thomas Wiecki</a>'''))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "papermill": {
     "duration": 0.350725,
     "end_time": "2020-03-21T08:21:37.316238",
     "exception": false,
     "start_time": "2020-03-21T08:21:36.965513",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
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       "    const outputDiv = document.getElementById(\"altair-viz-6cc2cf9655124091814e613b2c98a8b9\");\n",
       "    const paths = {\n",
       "      \"vega\": \"https://cdn.jsdelivr.net/npm//vega@5?noext\",\n",
       "      \"vega-lib\": \"https://cdn.jsdelivr.net/npm//vega-lib?noext\",\n",
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       "    function displayChart(vegaEmbed) {\n",
       "      vegaEmbed(outputDiv, spec, embedOpt)\n",
       "        .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
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       "\n",
       "    if(typeof define === \"function\" && define.amd) {\n",
       "      requirejs.config({paths});\n",
       "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
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\"United Kingdom\", \"Days\": 8, \"Confirmed\": 686, \"Confirmed/100k\": 1.2062147250813295}, {\"Country/Region\": \"United Kingdom\", \"Days\": 9, \"Confirmed\": 1028, \"Confirmed/100k\": 1.7205855928840912}, {\"Country/Region\": \"United Kingdom\", \"Days\": 10, \"Confirmed\": 1029, \"Confirmed/100k\": 1.7220896012694793}, {\"Country/Region\": \"United Kingdom\", \"Days\": 11, \"Confirmed\": 1435, \"Confirmed/100k\": 2.332717005737085}, {\"Country/Region\": \"United Kingdom\", \"Days\": 12, \"Confirmed\": 1844, \"Confirmed/100k\": 2.947856435360856}, {\"Country/Region\": \"United Kingdom\", \"Days\": 13, \"Confirmed\": 2526, \"Confirmed/100k\": 3.973590154195602}, {\"Country/Region\": \"United Kingdom\", \"Days\": 14, \"Confirmed\": 2600, \"Confirmed/100k\": 4.084886774714328}, {\"Country/Region\": \"United Kingdom\", \"Days\": 15, \"Confirmed\": 3898, \"Confirmed/100k\": null}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.VConcatChart(...)"
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     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
       "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
       "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
       "</p>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "sort_order = growth_in_value_df.groupby(\n",
    "    'Country/Region').max().sort_values(\n",
    "    'Confirmed', ascending=False).index.tolist()\n",
    "chart = facetted_growth_plot(increase_df, \n",
    "                             'Confirmed/100k',\n",
    "                             sort_order,\n",
    "                             'Italy',\n",
    "                             \"Growth of cases/100k from case 100, compared to Italy\")\n",
    "display(chart)\n",
    "display(HTML('''\n",
    "<p style=\"font-size: smaller\">Data Sources: \n",
    "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
    "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
    "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
    "</p>'''))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "papermill": {
     "duration": 0.388646,
     "end_time": "2020-03-21T08:21:37.736333",
     "exception": false,
     "start_time": "2020-03-21T08:21:37.347687",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "<div id=\"altair-viz-e69dfa2762804a7b846b16fe8366b26d\"></div>\n",
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       "  (function(spec, embedOpt){\n",
       "    const outputDiv = document.getElementById(\"altair-viz-e69dfa2762804a7b846b16fe8366b26d\");\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: ${paths[lib]}`);\n",
       "        document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
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       "    }\n",
       "\n",
       "    function showError(err) {\n",
       "      outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${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",
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       "      loadScript(\"vega\")\n",
       "        .then(() => loadScript(\"vega-lite\"))\n",
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\"Confirmed\": 3961, \"Confirmed/100k\": 47.84805290127696}, {\"Country/Region\": \"Switzerland\", \"Days\": 15, \"Confirmed\": 5180, \"Confirmed/100k\": null}, {\"Country/Region\": \"US\", \"Days\": 0, \"Confirmed\": 0, \"Confirmed/100k\": 0.03606715942271932}, {\"Country/Region\": \"US\", \"Days\": 1, \"Confirmed\": 31, \"Confirmed/100k\": 0.04554243011851846}, {\"Country/Region\": \"US\", \"Days\": 2, \"Confirmed\": 99, \"Confirmed/100k\": 0.06632689487059401}, {\"Country/Region\": \"US\", \"Days\": 3, \"Confirmed\": 144, \"Confirmed/100k\": 0.0800813200741734}, {\"Country/Region\": \"US\", \"Days\": 4, \"Confirmed\": 284, \"Confirmed/100k\": 0.122872865151976}, {\"Country/Region\": \"US\", \"Days\": 5, \"Confirmed\": 400, \"Confirmed/100k\": 0.15832871678786953}, {\"Country/Region\": \"US\", \"Days\": 6, \"Confirmed\": 465, \"Confirmed/100k\": 0.17819621985970646}, {\"Country/Region\": \"US\", \"Days\": 7, \"Confirmed\": 841, \"Confirmed/100k\": 0.2931220837829477}, {\"Country/Region\": \"US\", \"Days\": 8, \"Confirmed\": 1163, \"Confirmed/100k\": 0.3915426374618936}, {\"Country/Region\": \"US\", \"Days\": 9, \"Confirmed\": 1545, \"Confirmed/100k\": 0.508302424745612}, {\"Country/Region\": \"US\", \"Days\": 10, \"Confirmed\": 2061, \"Confirmed/100k\": 0.6660198337466559}, {\"Country/Region\": \"US\", \"Days\": 11, \"Confirmed\": 2609, \"Confirmed/100k\": 0.8335181673369116}, {\"Country/Region\": \"US\", \"Days\": 12, \"Confirmed\": 3381, \"Confirmed/100k\": 1.0694829730516515}, {\"Country/Region\": \"US\", \"Days\": 13, \"Confirmed\": 4514, \"Confirmed/100k\": 1.4157888342884395}, {\"Country/Region\": \"US\", \"Days\": 14, \"Confirmed\": 6303, \"Confirmed/100k\": 1.962603649604074}, {\"Country/Region\": \"US\", \"Days\": 15, \"Confirmed\": 7665, \"Confirmed/100k\": 2.3789042524324104}, {\"Country/Region\": \"US\", \"Days\": 16, \"Confirmed\": 13559, \"Confirmed/100k\": 4.1804283002078995}, {\"Country/Region\": \"US\", \"Days\": 17, \"Confirmed\": 18982, \"Confirmed/100k\": null}, {\"Country/Region\": \"United Kingdom\", \"Days\": 0, \"Confirmed\": 0, \"Confirmed/100k\": 0.17446497270503022}, {\"Country/Region\": \"United Kingdom\", \"Days\": 1, \"Confirmed\": 48, \"Confirmed/100k\": 0.2466573752036634}, {\"Country/Region\": \"United Kingdom\", \"Days\": 2, \"Confirmed\": 91, \"Confirmed/100k\": 0.3113297357753557}, {\"Country/Region\": \"United Kingdom\", \"Days\": 3, \"Confirmed\": 158, \"Confirmed/100k\": 0.4120982975963645}, {\"Country/Region\": \"United Kingdom\", \"Days\": 4, \"Confirmed\": 206, \"Confirmed/100k\": 0.4842907000949977}, {\"Country/Region\": \"United Kingdom\", \"Days\": 5, \"Confirmed\": 268, \"Confirmed/100k\": 0.5775392199890655}, {\"Country/Region\": \"United Kingdom\", \"Days\": 6, \"Confirmed\": 343, \"Confirmed/100k\": 0.6903398488931799}, {\"Country/Region\": \"United Kingdom\", \"Days\": 7, \"Confirmed\": 343, \"Confirmed/100k\": 0.6903398488931799}, {\"Country/Region\": \"United Kingdom\", \"Days\": 8, \"Confirmed\": 686, \"Confirmed/100k\": 1.2062147250813295}, {\"Country/Region\": \"United Kingdom\", \"Days\": 9, \"Confirmed\": 1028, \"Confirmed/100k\": 1.7205855928840912}, {\"Country/Region\": \"United Kingdom\", \"Days\": 10, \"Confirmed\": 1029, \"Confirmed/100k\": 1.7220896012694793}, {\"Country/Region\": \"United Kingdom\", \"Days\": 11, \"Confirmed\": 1435, \"Confirmed/100k\": 2.332717005737085}, {\"Country/Region\": \"United Kingdom\", \"Days\": 12, \"Confirmed\": 1844, \"Confirmed/100k\": 2.947856435360856}, {\"Country/Region\": \"United Kingdom\", \"Days\": 13, \"Confirmed\": 2526, \"Confirmed/100k\": 3.973590154195602}, {\"Country/Region\": \"United Kingdom\", \"Days\": 14, \"Confirmed\": 2600, \"Confirmed/100k\": 4.084886774714328}, {\"Country/Region\": \"United Kingdom\", \"Days\": 15, \"Confirmed\": 3898, \"Confirmed/100k\": null}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.VConcatChart(...)"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "<p style=\"font-size: smaller\">Data Sources: \n",
       "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
       "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",
       "  <a href=\"https://worldmap.harvard.edu/data/geonode:country_centroids_az8\">Harvard Worldmap</a>\n",
       "</p>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# Same with log scale\n",
    "sort_order = growth_in_value_df.groupby(\n",
    "    'Country/Region').max().sort_values(\n",
    "    'Confirmed', ascending=False).index.tolist()\n",
    "chart = facetted_growth_plot(increase_df, \n",
    "                             'Confirmed/100k',\n",
    "                             sort_order,\n",
    "                             'Italy',\n",
    "                             \"Growth of cases/100k from case 100, compared to Italy (log scale)\",\n",
    "                             'log')\n",
    "display(chart)\n",
    "display(HTML('''\n",
    "<p style=\"font-size: smaller\">Data Sources: \n",
    "  <a href=\"https://github.com/CSSEGISandData/COVID-19\">JHU CSSE</a>,\n",
    "  <a href=\"https://data.worldbank.org/indicator/SP.POP.TOTL\">World Bank</a>,\n",