Dashboard.run.ipynb

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   "outputs": [],
   "source": [
    "import pandas as pd\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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     "exception": false,
     "start_time": "2020-03-15T18:37:34.888271",
     "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"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
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     "duration": 0.020476,
     "end_time": "2020-03-15T18:37:34.939191",
     "exception": false,
     "start_time": "2020-03-15T18:37:34.918715",
     "status": "completed"
    },
    "tags": [
     "injected-parameters"
    ]
   },
   "outputs": [],
   "source": [
    "# Parameters\n",
    "PAPERMILL_INPUT_PATH = \"/tmp/fer34kve/notebooks/Dashboard.ipynb\"\n",
    "PAPERMILL_OUTPUT_PATH = \"runs/Dashboard.run.ipynb\"\n",
    "ts_folder = \"/tmp/fer34kve/data/covid-19_jhu-csse\"\n",
    "rates_folder = \"/tmp/fer34kve/data/covid-19_rates\"\n",
    "geodata_path = \"/tmp/fer34kve/data/geodata/geo_data.csv\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "papermill": {
     "duration": 0.019696,
     "end_time": "2020-03-15T18:37:34.967260",
     "exception": false,
     "start_time": "2020-03-15T18:37:34.947564",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "# Read in the data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "papermill": {
     "duration": 0.11357,
     "end_time": "2020-03-15T18:37:35.089592",
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     "start_time": "2020-03-15T18:37:34.976022",
     "status": "completed"
    },
    "tags": []
   },
   "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)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "papermill": {
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     "end_time": "2020-03-15T18:37:35.119478",
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     "start_time": "2020-03-15T18:37:35.108963",
     "status": "completed"
    },
    "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": {
    "papermill": {
     "duration": 0.043214,
     "end_time": "2020-03-15T18:37:35.170249",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.127035",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<em>Data up to Mar 14 2020; countries with 100 or more confirmed cases.</em>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "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": {
    "papermill": {
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     "end_time": "2020-03-15T18:37:35.196228",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.187277",
     "status": "completed"
    },
    "tags": []
   },
   "source": [
    "## How are cases per 100,000 distributed geographically?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "papermill": {
     "duration": 0.019124,
     "end_time": "2020-03-15T18:37:35.222813",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.203689",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "import altair as alt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "papermill": {
     "duration": 0.049232,
     "end_time": "2020-03-15T18:37:35.282648",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.233416",
     "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,
   "metadata": {
    "papermill": {
     "duration": 0.126646,
     "end_time": "2020-03-15T18:37:35.429936",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.303290",
     "status": "completed"
    },
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40.24448698}, {\"Country/Region\": \"Sweden\", \"Confirmed/100k\": 9.437135274607376, \"Deaths/100k\": 0.019640239905530446, \"Recovered/100k\": 0.009820119952765223, \"Confirmed\": 961.0, \"Deaths\": 2.0, \"Recovered\": 1.0, \"Long\": 16.74558049, \"Lat\": 62.77966519}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 15.957178869407455, \"Deaths/100k\": 0.15264409514517804, \"Recovered/100k\": 0.04696741389082401, \"Confirmed\": 1359.0, \"Deaths\": 13.0, \"Recovered\": 4.0, \"Long\": 8.20867471, \"Lat\": 46.79785878}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 0.8335181673369116, \"Deaths/100k\": 0.01650531024429528, \"Recovered/100k\": 0.0036678467209545055, \"Confirmed\": 2727.0, \"Deaths\": 54.0, \"Recovered\": 12.0, \"Long\": -112.4616737, \"Lat\": 45.6795472}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 1.719081584498703, \"Deaths/100k\": 0.031584176093152026, \"Recovered/100k\": 0.028576159322375637, \"Confirmed\": 1143.0, \"Deaths\": 21.0, \"Recovered\": 19.0, \"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": 0.097247,
     "end_time": "2020-03-15T18:37:35.544984",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.447737",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
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       "  (function(spec, embedOpt){\n",
       "    const outputDiv = document.getElementById(\"altair-viz-59f2d4843002481eb23decfa32046c7c\");\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: ${paths[lib]}`);\n",
       "        document.getElementsByTagName(\"head\")[0].appendChild(s);\n",
       "      });\n",
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       "\n",
       "    function showError(err) {\n",
       "      outputDiv.innerHTML = `<div class=\"error\" style=\"color:red;\">${err}</div>`;\n",
       "      throw err;\n",
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       "\n",
       "    function displayChart(vegaEmbed) {\n",
       "      vegaEmbed(outputDiv, spec, embedOpt)\n",
       "        .catch(err => showError(`Javascript Error: ${err.message}<br>This usually means there's a typo in your chart specification. See the javascript console for the full traceback.`));\n",
       "    }\n",
       "\n",
       "    if(typeof define === \"function\" && define.amd) {\n",
       "      requirejs.config({paths});\n",
       "      require([\"vega-embed\"], displayChart, err => showError(`Error loading script: ${err.message}`));\n",
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       "      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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-25.73288704}, {\"Country/Region\": \"Austria\", \"Confirmed/100k\": 7.403608688423027, \"Deaths/100k\": 0.01130321937163821, \"Recovered/100k\": 0.06781931622982926, \"Confirmed\": 655.0, \"Deaths\": 1.0, \"Recovered\": 6.0, \"Long\": 14.1264761, \"Lat\": 47.58549439}, {\"Country/Region\": \"Bahrain\", \"Confirmed/100k\": 13.380577391029535, \"Deaths/100k\": 0.0, \"Recovered/100k\": 2.8035495485966644, \"Confirmed\": 210.0, \"Deaths\": 0.0, \"Recovered\": 44.0, \"Long\": 50.54196932, \"Lat\": 26.04205135}, {\"Country/Region\": \"Belgium\", \"Confirmed/100k\": 6.0321826135162215, \"Deaths/100k\": 0.035019928090079665, \"Recovered/100k\": 0.008754982022519914, \"Confirmed\": 689.0, \"Deaths\": 4.0, \"Recovered\": 1.0, \"Long\": 4.64065114, \"Lat\": 50.63981576}, {\"Country/Region\": \"Brazil\", \"Confirmed/100k\": 0.07208692453324421, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 151.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": -53.09783113, \"Lat\": -10.78777702}, {\"Country/Region\": \"Canada\", \"Confirmed/100k\": 0.53428524615007, \"Deaths/100k\": 0.002698410334091263, \"Recovered/100k\": 0.021587282672730104, \"Confirmed\": 198.0, \"Deaths\": 1.0, \"Recovered\": 8.0, \"Long\": -98.30777028, \"Lat\": 61.36206324}, {\"Country/Region\": \"China\", \"Confirmed/100k\": 5.814264071284455, \"Deaths/100k\": 0.2292619531423894, \"Recovered/100k\": 4.7144816296051655, \"Confirmed\": 80977.0, \"Deaths\": 3193.0, \"Recovered\": 65660.0, \"Long\": 103.81907349, \"Lat\": 36.56176546}, {\"Country/Region\": \"Czechia\", \"Confirmed/100k\": 1.7787071810361583, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 189.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 15.31240163, \"Lat\": 49.73341233}, {\"Country/Region\": \"Denmark\", \"Confirmed/100k\": 14.420142938804432, \"Deaths/100k\": 0.01724897480718234, \"Recovered/100k\": 0.01724897480718234, \"Confirmed\": 836.0, \"Deaths\": 1.0, \"Recovered\": 1.0, \"Long\": 10.02800992, \"Lat\": 55.98125296}, {\"Country/Region\": \"Egypt\", \"Confirmed/100k\": 0.11074580236578434, \"Deaths/100k\": 0.002032033070931823, \"Recovered/100k\": 0.02743244645757961, \"Confirmed\": 109.0, \"Deaths\": 2.0, \"Recovered\": 27.0, \"Long\": 29.86190099, \"Lat\": 26.49593311}, {\"Country/Region\": \"Estonia\", \"Confirmed/100k\": 8.706290635665205, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0, \"Confirmed\": 115.0, \"Deaths\": 0.0, \"Recovered\": 0.0, \"Long\": 25.54248537, \"Lat\": 58.67192972}, {\"Country/Region\": \"Finland\", \"Confirmed/100k\": 4.077527387392285, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.018122343943965717, \"Confirmed\": 225.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 26.2746656, \"Lat\": 64.49884603}, {\"Country/Region\": \"France\", \"Confirmed/100k\": 6.687840449145809, \"Deaths/100k\": 0.13584675912327426, \"Recovered/100k\": 0.017913858345926282, \"Confirmed\": 4480.0, \"Deaths\": 91.0, \"Recovered\": 12.0, \"Long\": -2.76172945, \"Lat\": 42.17344011}, {\"Country/Region\": \"Germany\", \"Confirmed/100k\": 5.528897733624627, \"Deaths/100k\": 0.010852798168510723, \"Recovered/100k\": 0.055469857305721466, \"Confirmed\": 4585.0, \"Deaths\": 9.0, \"Recovered\": 46.0, \"Long\": 10.38578051, \"Lat\": 51.10698181}, {\"Country/Region\": \"Greece\", \"Confirmed/100k\": 2.1253454152384283, \"Deaths/100k\": 0.027965071253137214, \"Recovered/100k\": 0.07457352334169924, \"Confirmed\": 228.0, \"Deaths\": 3.0, \"Recovered\": 8.0, \"Long\": 22.95555794, \"Lat\": 39.07469623}, {\"Country/Region\": \"Iceland\", \"Confirmed/100k\": 44.1208912420031, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.28282622591027623, \"Confirmed\": 156.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": -18.57396167, \"Lat\": 64.99575386}, {\"Country/Region\": \"India\", \"Confirmed/100k\": 0.007540935480311991, \"Deaths/100k\": 0.00014786148000611743, \"Recovered/100k\": 0.00029572296001223485, \"Confirmed\": 102.0, \"Deaths\": 2.0, \"Recovered\": 4.0, \"Long\": 79.61197609999998, \"Lat\": 22.88578212}, {\"Country/Region\": \"Iran\", \"Confirmed/100k\": 15.561073521653087, \"Deaths/100k\": 0.7469413089582871, \"Recovered/100k\": 3.6173475175246668, \"Confirmed\": 12729.0, \"Deaths\": 611.0, \"Recovered\": 2959.0, \"Long\": 54.27407004, \"Lat\": 32.57503292}, {\"Country/Region\": \"Iraq\", \"Confirmed/100k\": 0.2862079014195912, \"Deaths/100k\": 0.026018900129053748, \"Recovered/100k\": 0.06764914033553975, \"Confirmed\": 110.0, \"Deaths\": 10.0, \"Recovered\": 26.0, \"Long\": 43.74353149, \"Lat\": 33.03970582}, {\"Country/Region\": \"Ireland\", \"Confirmed/100k\": 2.657872474042476, \"Deaths/100k\": 0.04120732517895311, \"Recovered/100k\": 0.0, \"Confirmed\": 129.0, \"Deaths\": 2.0, \"Recovered\": 0.0, \"Long\": -8.13793569, \"Lat\": 53.17544870000001}, {\"Country/Region\": \"Israel\", \"Confirmed/100k\": 2.1724937526734056, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.045025777257479915, \"Confirmed\": 193.0, \"Deaths\": 0.0, \"Recovered\": 4.0, \"Long\": 35.00444693, \"Lat\": 31.46110101}, {\"Country/Region\": \"Italy\", \"Confirmed/100k\": 35.0100129431308, \"Deaths/100k\": 2.3845265704519294, \"Recovered/100k\": 3.25328191360756, \"Confirmed\": 21157.0, \"Deaths\": 1441.0, \"Recovered\": 1966.0, \"Long\": 12.07001339, \"Lat\": 42.79662641}, {\"Country/Region\": \"Japan\", \"Confirmed/100k\": 0.6109266563976192, \"Deaths/100k\": 0.017387304580527327, \"Recovered/100k\": 0.09325917911373748, \"Confirmed\": 773.0, \"Deaths\": 22.0, \"Recovered\": 118.0, \"Long\": 138.03089558, \"Lat\": 37.59230135}, {\"Country/Region\": \"Korea, South\", \"Confirmed/100k\": 15.659842956913007, \"Deaths/100k\": 0.13943961079615835, \"Recovered/100k\": 0.9876972431394551, \"Confirmed\": 8086.0, \"Deaths\": 72.0, \"Recovered\": 510.0, \"Long\": 127.83916086, \"Lat\": 36.38523983}, {\"Country/Region\": \"Kuwait\", \"Confirmed/100k\": 2.513711206970521, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.1208515003351212, \"Confirmed\": 104.0, \"Deaths\": 0.0, \"Recovered\": 5.0, \"Long\": 47.58700459, \"Lat\": 29.33431262}, {\"Country/Region\": \"Malaysia\", \"Confirmed/100k\": 0.7548705404952363, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.11101037360224064, \"Confirmed\": 238.0, \"Deaths\": 0.0, \"Recovered\": 35.0, \"Long\": 109.69762284, \"Lat\": 3.78986846}, {\"Country/Region\": \"Netherlands\", \"Confirmed/100k\": 5.565544970444868, \"Deaths/100k\": 0.06964185573027988, \"Recovered/100k\": 0.011606975955046644, \"Confirmed\": 959.0, \"Deaths\": 12.0, \"Recovered\": 2.0, \"Long\": 5.28144793, \"Lat\": 52.1007899}, {\"Country/Region\": \"Norway\", \"Confirmed/100k\": 20.510558609767997, \"Deaths/100k\": 0.056451078742480724, \"Recovered/100k\": 0.018817026247493568, \"Confirmed\": 1090.0, \"Deaths\": 3.0, \"Recovered\": 1.0, \"Long\": 15.34834656, \"Lat\": 68.75015572}, {\"Country/Region\": \"Philippines\", \"Confirmed/100k\": 0.10407688667814162, \"Deaths/100k\": 0.007501036877703902, \"Recovered/100k\": 0.0018752592194259754, \"Confirmed\": 111.0, \"Deaths\": 8.0, \"Recovered\": 2.0, \"Long\": 122.88393253, \"Lat\": 11.77536778}, {\"Country/Region\": \"Poland\", \"Confirmed/100k\": 0.2712057343529827, \"Deaths/100k\": 0.007899196146203378, \"Recovered/100k\": 0.0, \"Confirmed\": 103.0, \"Deaths\": 3.0, \"Recovered\": 0.0, \"Long\": 19.39012835, \"Lat\": 52.12759564}, {\"Country/Region\": \"Portugal\", \"Confirmed/100k\": 1.6436871423399997, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.01945191884426035, \"Confirmed\": 169.0, \"Deaths\": 0.0, \"Recovered\": 2.0, \"Long\": -8.50104361, \"Lat\": 39.59550671}, {\"Country/Region\": \"Qatar\", \"Confirmed/100k\": 12.114993940705553, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.14379814766416085, \"Confirmed\": 337.0, \"Deaths\": 0.0, \"Recovered\": 4.0, \"Long\": 51.18479632, \"Lat\": 25.30601188}, {\"Country/Region\": \"Romania\", \"Confirmed/100k\": 0.6316134550303544, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.046215618660757636, \"Confirmed\": 123.0, \"Deaths\": 0.0, \"Recovered\": 9.0, \"Long\": 24.97293039, \"Lat\": 45.85243127}, {\"Country/Region\": \"Saudi Arabia\", \"Confirmed/100k\": 0.30563846287354696, \"Deaths/100k\": 0.0, \"Recovered/100k\": 0.0029673637172189025, \"Confirmed\": 103.0, \"Deaths\": 0.0, \"Recovered\": 1.0, \"Long\": 44.53686271, \"Lat\": 24.12245841}, {\"Country/Region\": \"Singapore\", \"Confirmed/100k\": 3.7597478557022965, \"Deaths/100k\": 0.0, \"Recovered/100k\": 1.8621392681544395, \"Confirmed\": 212.0, \"Deaths\": 0.0, \"Recovered\": 105.0, \"Long\": 103.81725592, \"Lat\": 1.35876087}, {\"Country/Region\": \"Slovenia\", \"Confirmed/100k\": 8.755076493248433, \"Deaths/100k\": 0.04837058836048858, \"Recovered/100k\": 0.0, \"Confirmed\": 181.0, \"Deaths\": 1.0, \"Recovered\": 0.0, \"Long\": 14.80444238, \"Lat\": 46.11554772}, {\"Country/Region\": \"Spain\", \"Confirmed/100k\": 13.678268839257742, \"Deaths/100k\": 0.4173466474190673, \"Recovered/100k\": 1.1065036754649118, \"Confirmed\": 6391.0, \"Deaths\": 195.0, \"Recovered\": 517.0, \"Long\": -3.64755047, \"Lat\": 40.24448698}, {\"Country/Region\": \"Sweden\", \"Confirmed/100k\": 9.437135274607376, \"Deaths/100k\": 0.019640239905530446, \"Recovered/100k\": 0.009820119952765223, \"Confirmed\": 961.0, \"Deaths\": 2.0, \"Recovered\": 1.0, \"Long\": 16.74558049, \"Lat\": 62.77966519}, {\"Country/Region\": \"Switzerland\", \"Confirmed/100k\": 15.957178869407455, \"Deaths/100k\": 0.15264409514517804, \"Recovered/100k\": 0.04696741389082401, \"Confirmed\": 1359.0, \"Deaths\": 13.0, \"Recovered\": 4.0, \"Long\": 8.20867471, \"Lat\": 46.79785878}, {\"Country/Region\": \"US\", \"Confirmed/100k\": 0.8335181673369116, \"Deaths/100k\": 0.01650531024429528, \"Recovered/100k\": 0.0036678467209545055, \"Confirmed\": 2727.0, \"Deaths\": 54.0, \"Recovered\": 12.0, \"Long\": -112.4616737, \"Lat\": 45.6795472}, {\"Country/Region\": \"United Kingdom\", \"Confirmed/100k\": 1.719081584498703, \"Deaths/100k\": 0.031584176093152026, \"Recovered/100k\": 0.028576159322375637, \"Confirmed\": 1143.0, \"Deaths\": 21.0, \"Recovered\": 19.0, \"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": 0.010252,
     "end_time": "2020-03-15T18:37:35.572988",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.562736",
     "status": "completed"
    },
    "tags": []
   },
   "source": [
    "## How have cases been growing?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "papermill": {
     "duration": 0.070855,
     "end_time": "2020-03-15T18:37:35.653535",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.582680",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [],
   "source": [
    "confirmed_rate_df = helper.growth_df(rates_frames_map, geodata_df, 'confirmed', countries_over_thresh)\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": 0.123355,
     "end_time": "2020-03-15T18:37:35.799231",
     "exception": false,
     "start_time": "2020-03-15T18:37:35.675876",
     "status": "completed"
    },
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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\"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-06T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-07T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-08T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-09T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-10T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-11T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-12T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-13T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-14T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-15T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-16T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-17T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-18T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-19T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-20T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-21T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-22T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-23T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-24T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-25T00:00:00\", \"Confirmed/100k\": 0.009820119952765223}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-26T00:00:00\", \"Confirmed/100k\": 0.019640239905530446}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-27T00:00:00\", \"Confirmed/100k\": 0.06874083966935657}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-28T00:00:00\", \"Confirmed/100k\": 0.06874083966935657}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-29T00:00:00\", \"Confirmed/100k\": 0.11784143943318268}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-01T00:00:00\", \"Confirmed/100k\": 0.13748167933871314}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-02T00:00:00\", \"Confirmed/100k\": 0.14730179929147835}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-03T00:00:00\", \"Confirmed/100k\": 0.20622251900806968}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-04T00:00:00\", \"Confirmed/100k\": 0.3437041983467828}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-05T00:00:00\", \"Confirmed/100k\": 0.923091275559931}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-06T00:00:00\", \"Confirmed/100k\": 0.9918321152292876}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-07T00:00:00\", \"Confirmed/100k\": 1.581039312395201}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-08T00:00:00\", \"Confirmed/100k\": 1.99348435041134}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-09T00:00:00\", \"Confirmed/100k\": 2.435389748285776}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-10T00:00:00\", \"Confirmed/100k\": 3.4861425832316537}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-11T00:00:00\", \"Confirmed/100k\": 4.9100599763826125}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-12T00:00:00\", \"Confirmed/100k\": 5.882251851706369}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-13T00:00:00\", \"Confirmed/100k\": 7.993577641550892}, {\"Country/Region\": \"Sweden\", \"Longitude\": 16.74558049, \"Latitude\": 62.77966519, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-14T00:00:00\", \"Confirmed/100k\": 9.437135274607376}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-22T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-23T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-24T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-25T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-26T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-27T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-28T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-29T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-30T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-01-31T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-01T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-02T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-03T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-04T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": 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\"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-11T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-12T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-13T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-14T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-15T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-16T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-17T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-18T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-19T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-20T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-21T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-22T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-23T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-24T00:00:00\", \"Confirmed/100k\": 0.0}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-25T00:00:00\", \"Confirmed/100k\": 0.011741853472706005}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-26T00:00:00\", \"Confirmed/100k\": 0.011741853472706005}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-27T00:00:00\", \"Confirmed/100k\": 0.09393482778164802}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-28T00:00:00\", \"Confirmed/100k\": 0.09393482778164802}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-02-29T00:00:00\", \"Confirmed/100k\": 0.21135336250870806}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-01T00:00:00\", \"Confirmed/100k\": 0.3170300437630621}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-02T00:00:00\", \"Confirmed/100k\": 0.4931578458536522}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-03T00:00:00\", \"Confirmed/100k\": 0.6575437944715362}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-04T00:00:00\", \"Confirmed/100k\": 1.0567668125435403}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-05T00:00:00\", \"Confirmed/100k\": 1.3385712958884843}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-06T00:00:00\", \"Confirmed/100k\": 2.5127566431590846}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-07T00:00:00\", \"Confirmed/100k\": 3.1468167306852086}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-08T00:00:00\", \"Confirmed/100k\": 3.957004620301923}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-09T00:00:00\", \"Confirmed/100k\": 4.391453198792045}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-10T00:00:00\", \"Confirmed/100k\": 5.7652500550986465}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-11T00:00:00\", \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-12T00:00:00\", \"Confirmed/100k\": 7.655688464204314}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-13T00:00:00\", \"Confirmed/100k\": 13.373971105412135}, {\"Country/Region\": \"Switzerland\", \"Longitude\": 8.20867471, \"Latitude\": 46.79785878, \"Geo Region\": \"Europe\", \"Date\": \"2020-03-14T00:00:00\", \"Confirmed/100k\": 15.957178869407455}]}}, {\"mode\": \"vega-lite\"});\n",
       "</script>"
      ],
      "text/plain": [
       "alt.Chart(...)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "base = alt.Chart(confirmed_rate_df).properties(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"
   ]
  }
 ],
 "metadata": {
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   "language": "python",
   "name": "python3"
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.7.6"
  },
  "papermill": {
   "duration": 2.560957,
   "end_time": "2020-03-15T18:37:36.125203",
   "environment_variables": {},
   "exception": null,
   "input_path": "/tmp/fer34kve/notebooks/Dashboard.ipynb",
   "output_path": "runs/Dashboard.run.ipynb",
   "parameters": {
    "PAPERMILL_INPUT_PATH": "/tmp/fer34kve/notebooks/Dashboard.ipynb",
    "PAPERMILL_OUTPUT_PATH": "runs/Dashboard.run.ipynb",
    "geodata_path": "/tmp/fer34kve/data/geodata/geo_data.csv",
    "rates_folder": "/tmp/fer34kve/data/covid-19_rates",
    "ts_folder": "/tmp/fer34kve/data/covid-19_jhu-csse"
   },
   "start_time": "2020-03-15T18:37:33.564246",
   "version": "1.1.0"
  }
 },
 "nbformat": 4,
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}