JHU_CSSE.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import bokeh\n",
    "from bokeh.models import ColumnDataSource\n",
    "from bokeh.plotting import figure\n",
    "from bokeh.io import output_notebook, show\n",
    "from bokeh.models.tools import HoverTool\n",
    "from bokeh.models import PrintfTickFormatter"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "url_cc = 'https://github.com/datasets/country-codes/raw/master/data/country-codes.csv'\n",
    "df_cc = pd.read_csv(url_cc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['FIFA', 'Dial', 'ISO3166-1-Alpha-3', 'MARC', 'is_independent',\n",
       "       'ISO3166-1-numeric', 'GAUL', 'FIPS', 'WMO', 'ISO3166-1-Alpha-2', 'ITU',\n",
       "       'IOC', 'DS', 'UNTERM Spanish Formal', 'Global Code',\n",
       "       'Intermediate Region Code', 'official_name_fr', 'UNTERM French Short',\n",
       "       'ISO4217-currency_name', 'Developed / Developing Countries',\n",
       "       'UNTERM Russian Formal', 'UNTERM English Short',\n",
       "       'ISO4217-currency_alphabetic_code',\n",
       "       'Small Island Developing States (SIDS)', 'UNTERM Spanish Short',\n",
       "       'ISO4217-currency_numeric_code', 'UNTERM Chinese Formal',\n",
       "       'UNTERM French Formal', 'UNTERM Russian Short', 'M49',\n",
       "       'Sub-region Code', 'Region Code', 'official_name_ar',\n",
       "       'ISO4217-currency_minor_unit', 'UNTERM Arabic Formal',\n",
       "       'UNTERM Chinese Short', 'Land Locked Developing Countries (LLDC)',\n",
       "       'Intermediate Region Name', 'official_name_es', 'UNTERM English Formal',\n",
       "       'official_name_cn', 'official_name_en', 'ISO4217-currency_country_name',\n",
       "       'Least Developed Countries (LDC)', 'Region Name', 'UNTERM Arabic Short',\n",
       "       'Sub-region Name', 'official_name_ru', 'Global Name', 'Capital',\n",
       "       'Continent', 'TLD', 'Languages', 'Geoname ID', 'CLDR display name',\n",
       "       'EDGAR'],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_cc.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "onm = list(pd.unique(df_cc['official_name_en']))[1:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "badctrcode = {'Brunei':'BRN','US':'USA','Iran':'IRN','Korea, South':'KOR','Vietnam':'VNM',\n",
    " 'Russia':'RUS','Moldova':'MDA','Bolivia':'BOL','United Kingdom':'GBR','Venezuela':'VEN'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "323127513"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "url_pop = 'https://github.com/datasets/population/raw/master/data/population.csv'\n",
    "df_pop = pd.read_csv(url_pop)\n",
    "df_pop.loc[(df_pop['Country Code']=='USA')].sort_values(by='Year').iloc[-1].Value.astype(int)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Country Name</th>\n",
       "      <th>Country Code</th>\n",
       "      <th>Year</th>\n",
       "      <th>Value</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Arab World</td>\n",
       "      <td>ARB</td>\n",
       "      <td>1960</td>\n",
       "      <td>92490932.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Arab World</td>\n",
       "      <td>ARB</td>\n",
       "      <td>1961</td>\n",
       "      <td>95044497.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Arab World</td>\n",
       "      <td>ARB</td>\n",
       "      <td>1962</td>\n",
       "      <td>97682294.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Arab World</td>\n",
       "      <td>ARB</td>\n",
       "      <td>1963</td>\n",
       "      <td>100411076.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Arab World</td>\n",
       "      <td>ARB</td>\n",
       "      <td>1964</td>\n",
       "      <td>103239902.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "  Country Name Country Code  Year        Value\n",
       "0   Arab World          ARB  1960   92490932.0\n",
       "1   Arab World          ARB  1961   95044497.0\n",
       "2   Arab World          ARB  1962   97682294.0\n",
       "3   Arab World          ARB  1963  100411076.0\n",
       "4   Arab World          ARB  1964  103239902.0"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_pop.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "# for ctr in list(pd.unique(df_pop['Country/Region'])):\n",
    "# #     print(ctr)\n",
    "#     if (df_cc['official_name_en']==ctr).sum()>0:\n",
    "#         ctr_code = df_cc.loc[df_cc['official_name_en']==ctr]['ISO3166-1-Alpha-3'].item()\n",
    "#     else:\n",
    "#         if ctr in badctrcode.keys():\n",
    "#             ctr_code = badctrcode[ctr]\n",
    "#             print(ctr,ctr_code)\n",
    "            \n",
    "#     if (df_pop['Country Code']==ctr_code).sum()>0:\n",
    "#         ctr_pop = df_pop.loc[(df_pop['Country Code']==ctr_code)].sort_values(by='Year').iloc[-1].Value.astype(int)\n",
    "#     else: \n",
    "#         pass # print(ctr)\n",
    "# #     print(ctr,ctr_pop)\n",
    "#             #             print(ctr_code,ctr,ctr_pop)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.style.use(\"fivethirtyeight\")   # ‘dark_background', ''bmh', 'grayscale', 'ggplot', 'fivethirtyeight'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_data():\n",
    "    ''' read data from JHU CSSE website and return the pandas dataframe\n",
    "    '''\n",
    "#     url = 'https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv'\n",
    "    url = 'https://github.com/CSSEGISandData/COVID-19/raw/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv'\n",
    "    df = pd.read_csv(url)\n",
    "    \n",
    "    return df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Province/State</th>\n",
       "      <th>Country/Region</th>\n",
       "      <th>Lat</th>\n",
       "      <th>Long</th>\n",
       "      <th>1/22/20</th>\n",
       "      <th>1/23/20</th>\n",
       "      <th>1/24/20</th>\n",
       "      <th>1/25/20</th>\n",
       "      <th>1/26/20</th>\n",
       "      <th>1/27/20</th>\n",
       "      <th>...</th>\n",
       "      <th>3/17/20</th>\n",
       "      <th>3/18/20</th>\n",
       "      <th>3/19/20</th>\n",
       "      <th>3/20/20</th>\n",
       "      <th>3/21/20</th>\n",
       "      <th>3/22/20</th>\n",
       "      <th>3/23/20</th>\n",
       "      <th>3/24/20</th>\n",
       "      <th>3/25/20</th>\n",
       "      <th>3/26/20</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Afghanistan</td>\n",
       "      <td>33.0000</td>\n",
       "      <td>65.0000</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>22</td>\n",
       "      <td>22</td>\n",
       "      <td>22</td>\n",
       "      <td>24</td>\n",
       "      <td>24</td>\n",
       "      <td>40</td>\n",
       "      <td>40</td>\n",
       "      <td>74</td>\n",
       "      <td>84</td>\n",
       "      <td>94</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Albania</td>\n",
       "      <td>41.1533</td>\n",
       "      <td>20.1683</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>55</td>\n",
       "      <td>59</td>\n",
       "      <td>64</td>\n",
       "      <td>70</td>\n",
       "      <td>76</td>\n",
       "      <td>89</td>\n",
       "      <td>104</td>\n",
       "      <td>123</td>\n",
       "      <td>146</td>\n",
       "      <td>174</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Algeria</td>\n",
       "      <td>28.0339</td>\n",
       "      <td>1.6596</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>60</td>\n",
       "      <td>74</td>\n",
       "      <td>87</td>\n",
       "      <td>90</td>\n",
       "      <td>139</td>\n",
       "      <td>201</td>\n",
       "      <td>230</td>\n",
       "      <td>264</td>\n",
       "      <td>302</td>\n",
       "      <td>367</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Andorra</td>\n",
       "      <td>42.5063</td>\n",
       "      <td>1.5218</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>39</td>\n",
       "      <td>39</td>\n",
       "      <td>53</td>\n",
       "      <td>75</td>\n",
       "      <td>88</td>\n",
       "      <td>113</td>\n",
       "      <td>133</td>\n",
       "      <td>164</td>\n",
       "      <td>188</td>\n",
       "      <td>224</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Angola</td>\n",
       "      <td>-11.2027</td>\n",
       "      <td>17.8739</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>3</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 69 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  Province/State Country/Region      Lat     Long  1/22/20  1/23/20  1/24/20  \\\n",
       "0            NaN    Afghanistan  33.0000  65.0000        0        0        0   \n",
       "1            NaN        Albania  41.1533  20.1683        0        0        0   \n",
       "2            NaN        Algeria  28.0339   1.6596        0        0        0   \n",
       "3            NaN        Andorra  42.5063   1.5218        0        0        0   \n",
       "4            NaN         Angola -11.2027  17.8739        0        0        0   \n",
       "\n",
       "   1/25/20  1/26/20  1/27/20  ...  3/17/20  3/18/20  3/19/20  3/20/20  \\\n",
       "0        0        0        0  ...       22       22       22       24   \n",
       "1        0        0        0  ...       55       59       64       70   \n",
       "2        0        0        0  ...       60       74       87       90   \n",
       "3        0        0        0  ...       39       39       53       75   \n",
       "4        0        0        0  ...        0        0        0        1   \n",
       "\n",
       "   3/21/20  3/22/20  3/23/20  3/24/20  3/25/20  3/26/20  \n",
       "0       24       40       40       74       84       94  \n",
       "1       76       89      104      123      146      174  \n",
       "2      139      201      230      264      302      367  \n",
       "3       88      113      133      164      188      224  \n",
       "4        2        2        3        3        3        4  \n",
       "\n",
       "[5 rows x 69 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = get_data()\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The last date of update is Mar 26, 2020\n"
     ]
    }
   ],
   "source": [
    "ltime = pd.Timestamp(df.columns[-1])\n",
    "print(f'The last date of update is {ltime:%b %d, %Y}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "def data_1cty(df, cty):\n",
    "    ''' derive country sum daily cases\n",
    "    \n",
    "    Parameters\n",
    "    ----------\n",
    "    df : pd dataframe\n",
    "        the input data\n",
    "    cty : str\n",
    "        the country name\n",
    "        \n",
    "    Returns\n",
    "    -------\n",
    "    series : pd Series\n",
    "        the total daily cases for the given country\n",
    "    '''\n",
    "    \n",
    "    filt = (df['Country/Region'] == cty)\n",
    "    nsts = filt.sum()\n",
    "    if nsts == 0:\n",
    "        return None\n",
    "    else:\n",
    "        series = df.loc[filt].iloc[:,4:].sum(axis=0)\n",
    "        series.index = pd.DatetimeIndex(series.index)\n",
    "        return series"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "def data_countries(df):\n",
    "    df_ctr = pd.DataFrame()    \n",
    "    str_ctrs = set(list(df['Country/Region'].values))\n",
    "    for ctr in str_ctrs:\n",
    "        df_ctr[ctr] = data_1cty(df, ctr)\n",
    "    return df_ctr"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_ctr = data_countries(df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "def plot_ctrs_ts(df_ctr, ctr_nm_all, colors=['blue', 'green', 'red', 'cyan', 'magenta', 'yellow'] ):\n",
    "    output_notebook()\n",
    "    source = ColumnDataSource(df_ctr)\n",
    "    \n",
    "    p = figure(plot_width=900, plot_height=500, x_axis_type='datetime',y_axis_type='log')\n",
    "    p.title.text = 'CoV19 cases'\n",
    "    p.xaxis.axis_label='Date'\n",
    "    p.yaxis.axis_label='Number of cases'\n",
    "    p.yaxis.formatter = PrintfTickFormatter(format=\"%5f\")\n",
    "    \n",
    "    for ctr_nm, c in zip(ctr_nm_all,colors):\n",
    "        p.line(x='index',y=ctr_nm,source=source, line_width=2, color=c, alpha=0.4)\n",
    "        ttp = [(\"date\", \"$x{%F}\"),(\"cases\", \"@\"+ctr_nm+\"{int}\"),(\"country\",ctr_nm)]        \n",
    "        cr = p.circle(x='index',y=ctr_nm,source=source,fill_color=c,size=8,alpha=0.4,line_color=None,\n",
    "                     hover_fill_color='firebrick',hover_line_color='firebrick',\n",
    "                     legend_label=ctr_nm, muted_color=c, muted_alpha=1)\n",
    "        fmt = {'$x': 'datetime'}\n",
    "        p.add_tools(HoverTool(tooltips=ttp, renderers=[cr],formatters=fmt))\n",
    "    \n",
    "    p.legend.location='top_left'\n",
    "    p.legend.click_policy='mute'\n",
    "    show(p)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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       "  var HTML_MIME_TYPE = 'text/html';\n",
       "  var EXEC_MIME_TYPE = 'application/vnd.bokehjs_exec.v0+json';\n",
       "  var CLASS_NAME = 'output_bokeh rendered_html';\n",
       "\n",
       "  /**\n",
       "   * Render data to the DOM node\n",
       "   */\n",
       "  function render(props, node) {\n",
       "    var script = document.createElement(\"script\");\n",
       "    node.appendChild(script);\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when an output is cleared or removed\n",
       "   */\n",
       "  function handleClearOutput(event, handle) {\n",
       "    var cell = handle.cell;\n",
       "\n",
       "    var id = cell.output_area._bokeh_element_id;\n",
       "    var server_id = cell.output_area._bokeh_server_id;\n",
       "    // Clean up Bokeh references\n",
       "    if (id != null && id in Bokeh.index) {\n",
       "      Bokeh.index[id].model.document.clear();\n",
       "      delete Bokeh.index[id];\n",
       "    }\n",
       "\n",
       "    if (server_id !== undefined) {\n",
       "      // Clean up Bokeh references\n",
       "      var cmd = \"from bokeh.io.state import curstate; print(curstate().uuid_to_server['\" + server_id + \"'].get_sessions()[0].document.roots[0]._id)\";\n",
       "      cell.notebook.kernel.execute(cmd, {\n",
       "        iopub: {\n",
       "          output: function(msg) {\n",
       "            var id = msg.content.text.trim();\n",
       "            if (id in Bokeh.index) {\n",
       "              Bokeh.index[id].model.document.clear();\n",
       "              delete Bokeh.index[id];\n",
       "            }\n",
       "          }\n",
       "        }\n",
       "      });\n",
       "      // Destroy server and session\n",
       "      var cmd = \"import bokeh.io.notebook as ion; ion.destroy_server('\" + server_id + \"')\";\n",
       "      cell.notebook.kernel.execute(cmd);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  /**\n",
       "   * Handle when a new output is added\n",
       "   */\n",
       "  function handleAddOutput(event, handle) {\n",
       "    var output_area = handle.output_area;\n",
       "    var output = handle.output;\n",
       "\n",
       "    // limit handleAddOutput to display_data with EXEC_MIME_TYPE content only\n",
       "    if ((output.output_type != \"display_data\") || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n",
       "      return\n",
       "    }\n",
       "\n",
       "    var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n",
       "\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"id\"] !== undefined) {\n",
       "      toinsert[toinsert.length - 1].firstChild.textContent = output.data[JS_MIME_TYPE];\n",
       "      // store reference to embed id on output_area\n",
       "      output_area._bokeh_element_id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n",
       "    }\n",
       "    if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n",
       "      var bk_div = document.createElement(\"div\");\n",
       "      bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n",
       "      var script_attrs = bk_div.children[0].attributes;\n",
       "      for (var i = 0; i < script_attrs.length; i++) {\n",
       "        toinsert[toinsert.length - 1].firstChild.setAttribute(script_attrs[i].name, script_attrs[i].value);\n",
       "      }\n",
       "      // store reference to server id on output_area\n",
       "      output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n",
       "    }\n",
       "  }\n",
       "\n",
       "  function register_renderer(events, OutputArea) {\n",
       "\n",
       "    function append_mime(data, metadata, element) {\n",
       "      // create a DOM node to render to\n",
       "      var toinsert = this.create_output_subarea(\n",
       "        metadata,\n",
       "        CLASS_NAME,\n",
       "        EXEC_MIME_TYPE\n",
       "      );\n",
       "      this.keyboard_manager.register_events(toinsert);\n",
       "      // Render to node\n",
       "      var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n",
       "      render(props, toinsert[toinsert.length - 1]);\n",
       "      element.append(toinsert);\n",
       "      return toinsert\n",
       "    }\n",
       "\n",
       "    /* Handle when an output is cleared or removed */\n",
       "    events.on('clear_output.CodeCell', handleClearOutput);\n",
       "    events.on('delete.Cell', handleClearOutput);\n",
       "\n",
       "    /* Handle when a new output is added */\n",
       "    events.on('output_added.OutputArea', handleAddOutput);\n",
       "\n",
       "    /**\n",
       "     * Register the mime type and append_mime function with output_area\n",
       "     */\n",
       "    OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n",
       "      /* Is output safe? */\n",
       "      safe: true,\n",
       "      /* Index of renderer in `output_area.display_order` */\n",
       "      index: 0\n",
       "    });\n",
       "  }\n",
       "\n",
       "  // register the mime type if in Jupyter Notebook environment and previously unregistered\n",
       "  if (root.Jupyter !== undefined) {\n",
       "    var events = require('base/js/events');\n",
       "    var OutputArea = require('notebook/js/outputarea').OutputArea;\n",
       "\n",
       "    if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n",
       "      register_renderer(events, OutputArea);\n",
       "    }\n",
       "  }\n",
       "\n",
       "  \n",
       "  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n",
       "    root._bokeh_timeout = Date.now() + 5000;\n",
       "    root._bokeh_failed_load = false;\n",
       "  }\n",
       "\n",
       "  var NB_LOAD_WARNING = {'data': {'text/html':\n",
       "     \"<div style='background-color: #fdd'>\\n\"+\n",
       "     \"<p>\\n\"+\n",
       "     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
       "     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
       "     \"</p>\\n\"+\n",
       "     \"<ul>\\n\"+\n",
       "     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n",
       "     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n",
       "     \"</ul>\\n\"+\n",
       "     \"<code>\\n\"+\n",
       "     \"from bokeh.resources import INLINE\\n\"+\n",
       "     \"output_notebook(resources=INLINE)\\n\"+\n",
       "     \"</code>\\n\"+\n",
       "     \"</div>\"}};\n",
       "\n",
       "  function display_loaded() {\n",
       "    var el = document.getElementById(\"1001\");\n",
       "    if (el != null) {\n",
       "      el.textContent = \"BokehJS is loading...\";\n",
       "    }\n",
       "    if (root.Bokeh !== undefined) {\n",
       "      if (el != null) {\n",
       "        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n",
       "      }\n",
       "    } else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(display_loaded, 100)\n",
       "    }\n",
       "  }\n",
       "\n",
       "\n",
       "  function run_callbacks() {\n",
       "    try {\n",
       "      root._bokeh_onload_callbacks.forEach(function(callback) {\n",
       "        if (callback != null)\n",
       "          callback();\n",
       "      });\n",
       "    } finally {\n",
       "      delete root._bokeh_onload_callbacks\n",
       "    }\n",
       "    console.debug(\"Bokeh: all callbacks have finished\");\n",
       "  }\n",
       "\n",
       "  function load_libs(css_urls, js_urls, callback) {\n",
       "    if (css_urls == null) css_urls = [];\n",
       "    if (js_urls == null) js_urls = [];\n",
       "\n",
       "    root._bokeh_onload_callbacks.push(callback);\n",
       "    if (root._bokeh_is_loading > 0) {\n",
       "      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n",
       "      return null;\n",
       "    }\n",
       "    if (js_urls == null || js_urls.length === 0) {\n",
       "      run_callbacks();\n",
       "      return null;\n",
       "    }\n",
       "    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n",
       "    root._bokeh_is_loading = css_urls.length + js_urls.length;\n",
       "\n",
       "    function on_load() {\n",
       "      root._bokeh_is_loading--;\n",
       "      if (root._bokeh_is_loading === 0) {\n",
       "        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n",
       "        run_callbacks()\n",
       "      }\n",
       "    }\n",
       "\n",
       "    function on_error() {\n",
       "      console.error(\"failed to load \" + url);\n",
       "    }\n",
       "\n",
       "    for (var i = 0; i < css_urls.length; i++) {\n",
       "      var url = css_urls[i];\n",
       "      const element = document.createElement(\"link\");\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error;\n",
       "      element.rel = \"stylesheet\";\n",
       "      element.type = \"text/css\";\n",
       "      element.href = url;\n",
       "      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n",
       "      document.body.appendChild(element);\n",
       "    }\n",
       "\n",
       "    for (var i = 0; i < js_urls.length; i++) {\n",
       "      var url = js_urls[i];\n",
       "      var element = document.createElement('script');\n",
       "      element.onload = on_load;\n",
       "      element.onerror = on_error;\n",
       "      element.async = false;\n",
       "      element.src = url;\n",
       "      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n",
       "      document.head.appendChild(element);\n",
       "    }\n",
       "  };var element = document.getElementById(\"1001\");\n",
       "  if (element == null) {\n",
       "    console.error(\"Bokeh: ERROR: autoload.js configured with elementid '1001' but no matching script tag was found. \")\n",
       "    return false;\n",
       "  }\n",
       "\n",
       "  function inject_raw_css(css) {\n",
       "    const element = document.createElement(\"style\");\n",
       "    element.appendChild(document.createTextNode(css));\n",
       "    document.body.appendChild(element);\n",
       "  }\n",
       "\n",
       "  \n",
       "  var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-1.4.0.min.js\"];\n",
       "  var css_urls = [];\n",
       "  \n",
       "\n",
       "  var inline_js = [\n",
       "    function(Bokeh) {\n",
       "      Bokeh.set_log_level(\"info\");\n",
       "    },\n",
       "    function(Bokeh) {\n",
       "    \n",
       "    \n",
       "    }\n",
       "  ];\n",
       "\n",
       "  function run_inline_js() {\n",
       "    \n",
       "    if (root.Bokeh !== undefined || force === true) {\n",
       "      \n",
       "    for (var i = 0; i < inline_js.length; i++) {\n",
       "      inline_js[i].call(root, root.Bokeh);\n",
       "    }\n",
       "    if (force === true) {\n",
       "        display_loaded();\n",
       "      }} else if (Date.now() < root._bokeh_timeout) {\n",
       "      setTimeout(run_inline_js, 100);\n",
       "    } else if (!root._bokeh_failed_load) {\n",
       "      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n",
       "      root._bokeh_failed_load = true;\n",
       "    } else if (force !== true) {\n",
       "      var cell = $(document.getElementById(\"1001\")).parents('.cell').data().cell;\n",
       "      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n",
       "    }\n",
       "\n",
       "  }\n",
       "\n",
       "  if (root._bokeh_is_loading === 0) {\n",
       "    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n",
       "    run_inline_js();\n",
       "  } else {\n",
       "    load_libs(css_urls, js_urls, function() {\n",
       "      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n",
       "      run_inline_js();\n",
       "    });\n",
       "  }\n",
       "}(window));"
      ],
      "application/vnd.bokehjs_load.v0+json": "\n(function(root) {\n  function now() {\n    return new Date();\n  }\n\n  var force = true;\n\n  if (typeof root._bokeh_onload_callbacks === \"undefined\" || force === true) {\n    root._bokeh_onload_callbacks = [];\n    root._bokeh_is_loading = undefined;\n  }\n\n  \n\n  \n  if (typeof (root._bokeh_timeout) === \"undefined\" || force === true) {\n    root._bokeh_timeout = Date.now() + 5000;\n    root._bokeh_failed_load = false;\n  }\n\n  var NB_LOAD_WARNING = {'data': {'text/html':\n     \"<div style='background-color: #fdd'>\\n\"+\n     \"<p>\\n\"+\n     \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n     \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n     \"</p>\\n\"+\n     \"<ul>\\n\"+\n     \"<li>re-rerun `output_notebook()` to attempt to load from CDN again, or</li>\\n\"+\n     \"<li>use INLINE resources instead, as so:</li>\\n\"+\n     \"</ul>\\n\"+\n     \"<code>\\n\"+\n     \"from bokeh.resources import INLINE\\n\"+\n     \"output_notebook(resources=INLINE)\\n\"+\n     \"</code>\\n\"+\n     \"</div>\"}};\n\n  function display_loaded() {\n    var el = document.getElementById(\"1001\");\n    if (el != null) {\n      el.textContent = \"BokehJS is loading...\";\n    }\n    if (root.Bokeh !== undefined) {\n      if (el != null) {\n        el.textContent = \"BokehJS \" + root.Bokeh.version + \" successfully loaded.\";\n      }\n    } else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(display_loaded, 100)\n    }\n  }\n\n\n  function run_callbacks() {\n    try {\n      root._bokeh_onload_callbacks.forEach(function(callback) {\n        if (callback != null)\n          callback();\n      });\n    } finally {\n      delete root._bokeh_onload_callbacks\n    }\n    console.debug(\"Bokeh: all callbacks have finished\");\n  }\n\n  function load_libs(css_urls, js_urls, callback) {\n    if (css_urls == null) css_urls = [];\n    if (js_urls == null) js_urls = [];\n\n    root._bokeh_onload_callbacks.push(callback);\n    if (root._bokeh_is_loading > 0) {\n      console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n      return null;\n    }\n    if (js_urls == null || js_urls.length === 0) {\n      run_callbacks();\n      return null;\n    }\n    console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n    root._bokeh_is_loading = css_urls.length + js_urls.length;\n\n    function on_load() {\n      root._bokeh_is_loading--;\n      if (root._bokeh_is_loading === 0) {\n        console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n        run_callbacks()\n      }\n    }\n\n    function on_error() {\n      console.error(\"failed to load \" + url);\n    }\n\n    for (var i = 0; i < css_urls.length; i++) {\n      var url = css_urls[i];\n      const element = document.createElement(\"link\");\n      element.onload = on_load;\n      element.onerror = on_error;\n      element.rel = \"stylesheet\";\n      element.type = \"text/css\";\n      element.href = url;\n      console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n      document.body.appendChild(element);\n    }\n\n    for (var i = 0; i < js_urls.length; i++) {\n      var url = js_urls[i];\n      var element = document.createElement('script');\n      element.onload = on_load;\n      element.onerror = on_error;\n      element.async = false;\n      element.src = url;\n      console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n      document.head.appendChild(element);\n    }\n  };var element = document.getElementById(\"1001\");\n  if (element == null) {\n    console.error(\"Bokeh: ERROR: autoload.js configured with elementid '1001' but no matching script tag was found. \")\n    return false;\n  }\n\n  function inject_raw_css(css) {\n    const element = document.createElement(\"style\");\n    element.appendChild(document.createTextNode(css));\n    document.body.appendChild(element);\n  }\n\n  \n  var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-tables-1.4.0.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-gl-1.4.0.min.js\"];\n  var css_urls = [];\n  \n\n  var inline_js = [\n    function(Bokeh) {\n      Bokeh.set_log_level(\"info\");\n    },\n    function(Bokeh) {\n    \n    \n    }\n  ];\n\n  function run_inline_js() {\n    \n    if (root.Bokeh !== undefined || force === true) {\n      \n    for (var i = 0; i < inline_js.length; i++) {\n      inline_js[i].call(root, root.Bokeh);\n    }\n    if (force === true) {\n        display_loaded();\n      }} else if (Date.now() < root._bokeh_timeout) {\n      setTimeout(run_inline_js, 100);\n    } else if (!root._bokeh_failed_load) {\n      console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n      root._bokeh_failed_load = true;\n    } else if (force !== true) {\n      var cell = $(document.getElementById(\"1001\")).parents('.cell').data().cell;\n      cell.output_area.append_execute_result(NB_LOAD_WARNING)\n    }\n\n  }\n\n  if (root._bokeh_is_loading === 0) {\n    console.debug(\"Bokeh: BokehJS loaded, going straight to plotting\");\n    run_inline_js();\n  } else {\n    load_libs(css_urls, js_urls, function() {\n      console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n      run_inline_js();\n    });\n  }\n}(window));"
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "\n",
       "  <div class=\"bk-root\" id=\"3367a705-99c0-4dc3-a386-bef5699a64a7\" data-root-id=\"1003\"></div>\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "(function(root) {\n",
       "  function embed_document(root) {\n",
       "    \n",
       "  var docs_json = 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       "  var render_items = [{\"docid\":\"9e6c4ed6-e1d7-4be0-aec3-b2abd44a9d22\",\"roots\":{\"1003\":\"3367a705-99c0-4dc3-a386-bef5699a64a7\"}}];\n",
       "  root.Bokeh.embed.embed_items_notebook(docs_json, render_items);\n",
       "\n",
       "  }\n",
       "  if (root.Bokeh !== undefined) {\n",
       "    embed_document(root);\n",
       "  } else {\n",
       "    var attempts = 0;\n",
       "    var timer = setInterval(function(root) {\n",
       "      if (root.Bokeh !== undefined) {\n",
       "        clearInterval(timer);\n",
       "        embed_document(root);\n",
       "      } else {\n",
       "        attempts++;\n",
       "        if (attempts > 100) {\n",
       "          clearInterval(timer);\n",
       "          console.log(\"Bokeh: ERROR: Unable to run BokehJS code because BokehJS library is missing\");\n",
       "        }\n",
       "      }\n",
       "    }, 10, root)\n",
       "  }\n",
       "})(window);"
      ],
      "application/vnd.bokehjs_exec.v0+json": ""
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "id": "1003"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "plot_ctrs_ts(df_ctr, ['US','Italy','Spain'])"
   ]
  }
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