JHU_COVIDSpread_DataAcquisition.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Data Extraction of COVID-19 spread"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<style>.container { width:95% !important; }</style>"
      ],
      "text/plain": [
       "<IPython.core.display.HTML object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from IPython.core.display import display, HTML,display_html\n",
    "display(HTML(\"<style>.container { width:95% !important; }</style>\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "confirmed_df= pd.read_csv('https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_confirmed_global.csv')\n",
    "deaths_df = pd.read_csv('https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv')\n",
    "recovered_df = pd.read_csv('https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_recovered_global.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\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>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>5/14/20</th>\n",
       "      <th>5/15/20</th>\n",
       "      <th>5/16/20</th>\n",
       "      <th>5/17/20</th>\n",
       "      <th>5/18/20</th>\n",
       "      <th>5/19/20</th>\n",
       "      <th>5/20/20</th>\n",
       "      <th>5/21/20</th>\n",
       "      <th>5/22/20</th>\n",
       "      <th>5/23/20</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>5639</td>\n",
       "      <td>6053</td>\n",
       "      <td>6402</td>\n",
       "      <td>6664</td>\n",
       "      <td>7072</td>\n",
       "      <td>7653</td>\n",
       "      <td>8145</td>\n",
       "      <td>8676</td>\n",
       "      <td>9216</td>\n",
       "      <td>9998</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>898</td>\n",
       "      <td>916</td>\n",
       "      <td>933</td>\n",
       "      <td>946</td>\n",
       "      <td>948</td>\n",
       "      <td>949</td>\n",
       "      <td>964</td>\n",
       "      <td>969</td>\n",
       "      <td>981</td>\n",
       "      <td>989</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>6442</td>\n",
       "      <td>6629</td>\n",
       "      <td>6821</td>\n",
       "      <td>7019</td>\n",
       "      <td>7201</td>\n",
       "      <td>7377</td>\n",
       "      <td>7542</td>\n",
       "      <td>7728</td>\n",
       "      <td>7918</td>\n",
       "      <td>8113</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>761</td>\n",
       "      <td>761</td>\n",
       "      <td>761</td>\n",
       "      <td>761</td>\n",
       "      <td>761</td>\n",
       "      <td>761</td>\n",
       "      <td>762</td>\n",
       "      <td>762</td>\n",
       "      <td>762</td>\n",
       "      <td>762</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>48</td>\n",
       "      <td>48</td>\n",
       "      <td>48</td>\n",
       "      <td>48</td>\n",
       "      <td>50</td>\n",
       "      <td>52</td>\n",
       "      <td>52</td>\n",
       "      <td>58</td>\n",
       "      <td>60</td>\n",
       "      <td>61</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 127 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  ...  5/14/20  5/15/20  5/16/20  5/17/20  \\\n",
       "0        0        0        0  ...     5639     6053     6402     6664   \n",
       "1        0        0        0  ...      898      916      933      946   \n",
       "2        0        0        0  ...     6442     6629     6821     7019   \n",
       "3        0        0        0  ...      761      761      761      761   \n",
       "4        0        0        0  ...       48       48       48       48   \n",
       "\n",
       "   5/18/20  5/19/20  5/20/20  5/21/20  5/22/20  5/23/20  \n",
       "0     7072     7653     8145     8676     9216     9998  \n",
       "1      948      949      964      969      981      989  \n",
       "2     7201     7377     7542     7728     7918     8113  \n",
       "3      761      761      762      762      762      762  \n",
       "4       50       52       52       58       60       61  \n",
       "\n",
       "[5 rows x 127 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "confirmed_df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "dates = confirmed_df.columns[4:]\n",
    "\n",
    "confirmed_df_long = confirmed_df.melt(\n",
    "    id_vars=['Province/State', 'Country/Region', 'Lat', 'Long'], \n",
    "    value_vars=dates, \n",
    "    var_name='Date', \n",
    "    value_name='Confirmed'\n",
    ")\n",
    "deaths_df_long = deaths_df.melt(\n",
    "    id_vars=['Province/State', 'Country/Region', 'Lat', 'Long'], \n",
    "    value_vars=dates, \n",
    "    var_name='Date', \n",
    "    value_name='Deaths'\n",
    ")\n",
    "recovered_df_long = recovered_df.melt(\n",
    "    id_vars=['Province/State', 'Country/Region', 'Lat', 'Long'], \n",
    "    value_vars=dates, \n",
    "    var_name='Date', \n",
    "    value_name='Recovered'\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\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>Province/State</th>\n",
       "      <th>Country/Region</th>\n",
       "      <th>Lat</th>\n",
       "      <th>Long</th>\n",
       "      <th>Date</th>\n",
       "      <th>Confirmed</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Afghanistan</td>\n",
       "      <td>33.000000</td>\n",
       "      <td>65.000000</td>\n",
       "      <td>1/22/20</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Albania</td>\n",
       "      <td>41.153300</td>\n",
       "      <td>20.168300</td>\n",
       "      <td>1/22/20</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Algeria</td>\n",
       "      <td>28.033900</td>\n",
       "      <td>1.659600</td>\n",
       "      <td>1/22/20</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Andorra</td>\n",
       "      <td>42.506300</td>\n",
       "      <td>1.521800</td>\n",
       "      <td>1/22/20</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Angola</td>\n",
       "      <td>-11.202700</td>\n",
       "      <td>17.873900</td>\n",
       "      <td>1/22/20</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32713</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Sao Tome and Principe</td>\n",
       "      <td>0.186360</td>\n",
       "      <td>6.613081</td>\n",
       "      <td>5/23/20</td>\n",
       "      <td>251</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32714</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Yemen</td>\n",
       "      <td>15.552727</td>\n",
       "      <td>48.516388</td>\n",
       "      <td>5/23/20</td>\n",
       "      <td>212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32715</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Comoros</td>\n",
       "      <td>-11.645500</td>\n",
       "      <td>43.333300</td>\n",
       "      <td>5/23/20</td>\n",
       "      <td>78</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32716</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Tajikistan</td>\n",
       "      <td>38.861034</td>\n",
       "      <td>71.276093</td>\n",
       "      <td>5/23/20</td>\n",
       "      <td>2738</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32717</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Lesotho</td>\n",
       "      <td>-29.609988</td>\n",
       "      <td>28.233608</td>\n",
       "      <td>5/23/20</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>32718 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Province/State         Country/Region        Lat       Long     Date  \\\n",
       "0                NaN            Afghanistan  33.000000  65.000000  1/22/20   \n",
       "1                NaN                Albania  41.153300  20.168300  1/22/20   \n",
       "2                NaN                Algeria  28.033900   1.659600  1/22/20   \n",
       "3                NaN                Andorra  42.506300   1.521800  1/22/20   \n",
       "4                NaN                 Angola -11.202700  17.873900  1/22/20   \n",
       "...              ...                    ...        ...        ...      ...   \n",
       "32713            NaN  Sao Tome and Principe   0.186360   6.613081  5/23/20   \n",
       "32714            NaN                  Yemen  15.552727  48.516388  5/23/20   \n",
       "32715            NaN                Comoros -11.645500  43.333300  5/23/20   \n",
       "32716            NaN             Tajikistan  38.861034  71.276093  5/23/20   \n",
       "32717            NaN                Lesotho -29.609988  28.233608  5/23/20   \n",
       "\n",
       "       Confirmed  \n",
       "0              0  \n",
       "1              0  \n",
       "2              0  \n",
       "3              0  \n",
       "4              0  \n",
       "...          ...  \n",
       "32713        251  \n",
       "32714        212  \n",
       "32715         78  \n",
       "32716       2738  \n",
       "32717          2  \n",
       "\n",
       "[32718 rows x 6 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "confirmed_df_long"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Remove Canada from df as recovered data is counted by Country-wise rather than Province/State-wise\n",
    "recovered_df_long = recovered_df_long[recovered_df_long['Country/Region']!='Canada']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Merging confirmed_df_long and deaths_df_long\n",
    "full_table = confirmed_df_long.merge(\n",
    "  right=deaths_df_long, \n",
    "  how='left',\n",
    "  on=['Province/State', 'Country/Region', 'Date', 'Lat', 'Long']\n",
    ")\n",
    "# Merging full_table and recovered_df_long\n",
    "full_table = full_table.merge(\n",
    "  right=recovered_df_long, \n",
    "  how='left',\n",
    "  on=['Province/State', 'Country/Region', 'Date', 'Lat', 'Long']\n",
    ")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "full_table['Date'] = pd.to_datetime(full_table['Date'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Province/State    22755\n",
       "Country/Region        0\n",
       "Lat                   0\n",
       "Long                  0\n",
       "Date                  0\n",
       "Confirmed             0\n",
       "Deaths                0\n",
       "Recovered          3444\n",
       "dtype: int64"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Check for missing values\n",
    "full_table.isna().sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "full_table['Recovered'] = full_table['Recovered'].fillna(0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Identify data of ship rows\n",
    "ship_rows = full_table['Province/State'].str.contains('Grand Princess') | full_table['Province/State'].str.contains('Diamond Princess') | full_table['Country/Region'].str.contains('Diamond Princess') | full_table['Country/Region'].str.contains('MS Zaandam')\n",
    "full_ship = full_table[ship_rows]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "## Remove rows containing COVID 19 spread on ships\n",
    "full_table = full_table[~(ship_rows)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<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>Date</th>\n",
       "      <th>Confirmed</th>\n",
       "      <th>Deaths</th>\n",
       "      <th>Recovered</th>\n",
       "      <th>Active</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Afghanistan</td>\n",
       "      <td>33.000000</td>\n",
       "      <td>65.000000</td>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Albania</td>\n",
       "      <td>41.153300</td>\n",
       "      <td>20.168300</td>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Algeria</td>\n",
       "      <td>28.033900</td>\n",
       "      <td>1.659600</td>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Andorra</td>\n",
       "      <td>42.506300</td>\n",
       "      <td>1.521800</td>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Angola</td>\n",
       "      <td>-11.202700</td>\n",
       "      <td>17.873900</td>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32713</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Sao Tome and Principe</td>\n",
       "      <td>0.186360</td>\n",
       "      <td>6.613081</td>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>251</td>\n",
       "      <td>8</td>\n",
       "      <td>4.0</td>\n",
       "      <td>239.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32714</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Yemen</td>\n",
       "      <td>15.552727</td>\n",
       "      <td>48.516388</td>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>212</td>\n",
       "      <td>39</td>\n",
       "      <td>0.0</td>\n",
       "      <td>173.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32715</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Comoros</td>\n",
       "      <td>-11.645500</td>\n",
       "      <td>43.333300</td>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>78</td>\n",
       "      <td>1</td>\n",
       "      <td>18.0</td>\n",
       "      <td>59.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32716</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Tajikistan</td>\n",
       "      <td>38.861034</td>\n",
       "      <td>71.276093</td>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>2738</td>\n",
       "      <td>44</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2694.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32717</th>\n",
       "      <td>NaN</td>\n",
       "      <td>Lesotho</td>\n",
       "      <td>-29.609988</td>\n",
       "      <td>28.233608</td>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>32226 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      Province/State         Country/Region        Lat       Long       Date  \\\n",
       "0                NaN            Afghanistan  33.000000  65.000000 2020-01-22   \n",
       "1                NaN                Albania  41.153300  20.168300 2020-01-22   \n",
       "2                NaN                Algeria  28.033900   1.659600 2020-01-22   \n",
       "3                NaN                Andorra  42.506300   1.521800 2020-01-22   \n",
       "4                NaN                 Angola -11.202700  17.873900 2020-01-22   \n",
       "...              ...                    ...        ...        ...        ...   \n",
       "32713            NaN  Sao Tome and Principe   0.186360   6.613081 2020-05-23   \n",
       "32714            NaN                  Yemen  15.552727  48.516388 2020-05-23   \n",
       "32715            NaN                Comoros -11.645500  43.333300 2020-05-23   \n",
       "32716            NaN             Tajikistan  38.861034  71.276093 2020-05-23   \n",
       "32717            NaN                Lesotho -29.609988  28.233608 2020-05-23   \n",
       "\n",
       "       Confirmed  Deaths  Recovered  Active  \n",
       "0              0       0        0.0     0.0  \n",
       "1              0       0        0.0     0.0  \n",
       "2              0       0        0.0     0.0  \n",
       "3              0       0        0.0     0.0  \n",
       "4              0       0        0.0     0.0  \n",
       "...          ...     ...        ...     ...  \n",
       "32713        251       8        4.0   239.0  \n",
       "32714        212      39        0.0   173.0  \n",
       "32715         78       1       18.0    59.0  \n",
       "32716       2738      44        0.0  2694.0  \n",
       "32717          2       0        0.0     2.0  \n",
       "\n",
       "[32226 rows x 9 columns]"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Active Case = confirmed - deaths - recovered\n",
    "full_table['Active'] = full_table['Confirmed'] - full_table['Deaths'] - full_table['Recovered']\n",
    "full_table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\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>Date</th>\n",
       "      <th>Country/Region</th>\n",
       "      <th>Confirmed</th>\n",
       "      <th>Deaths</th>\n",
       "      <th>Recovered</th>\n",
       "      <th>Active</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>Afghanistan</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>Albania</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>Algeria</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>Andorra</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>Angola</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22873</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>West Bank and Gaza</td>\n",
       "      <td>423</td>\n",
       "      <td>3</td>\n",
       "      <td>348.0</td>\n",
       "      <td>72.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22874</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Western Sahara</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22875</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Yemen</td>\n",
       "      <td>212</td>\n",
       "      <td>39</td>\n",
       "      <td>0.0</td>\n",
       "      <td>173.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22876</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Zambia</td>\n",
       "      <td>920</td>\n",
       "      <td>7</td>\n",
       "      <td>336.0</td>\n",
       "      <td>577.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22877</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Zimbabwe</td>\n",
       "      <td>56</td>\n",
       "      <td>4</td>\n",
       "      <td>18.0</td>\n",
       "      <td>34.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>22878 rows × 6 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Date      Country/Region  Confirmed  Deaths  Recovered  Active\n",
       "0     2020-01-22         Afghanistan          0       0        0.0     0.0\n",
       "1     2020-01-22             Albania          0       0        0.0     0.0\n",
       "2     2020-01-22             Algeria          0       0        0.0     0.0\n",
       "3     2020-01-22             Andorra          0       0        0.0     0.0\n",
       "4     2020-01-22              Angola          0       0        0.0     0.0\n",
       "...          ...                 ...        ...     ...        ...     ...\n",
       "22873 2020-05-23  West Bank and Gaza        423       3      348.0    72.0\n",
       "22874 2020-05-23      Western Sahara          6       0        6.0     0.0\n",
       "22875 2020-05-23               Yemen        212      39        0.0   173.0\n",
       "22876 2020-05-23              Zambia        920       7      336.0   577.0\n",
       "22877 2020-05-23            Zimbabwe         56       4       18.0    34.0\n",
       "\n",
       "[22878 rows x 6 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# aggregate data into Country/Region wise and group them by Date and Country/Region.\n",
    "full_grouped = full_table.groupby(['Date', 'Country/Region'])[['Confirmed', 'Deaths', 'Recovered', 'Active']].sum().reset_index()\n",
    "full_grouped"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# new cases \n",
    "temp = full_grouped.groupby(['Country/Region', 'Date' ])[['Confirmed', 'Deaths', 'Recovered']]\n",
    "temp = temp.sum().diff().reset_index()\n",
    "mask = temp['Country/Region'] != temp['Country/Region'].shift(1)\n",
    "temp.loc[mask, 'Confirmed'] = np.nan\n",
    "temp.loc[mask, 'Deaths'] = np.nan\n",
    "temp.loc[mask, 'Recovered'] = np.nan\n",
    "# renaming columns\n",
    "temp.columns = ['Country/Region', 'Date', 'New cases', 'New deaths', 'New recovered']\n",
    "# merging new values\n",
    "full_grouped = pd.merge(full_grouped, temp, on=['Country/Region', 'Date'])\n",
    "# filling na with 0\n",
    "full_grouped = full_grouped.fillna(0)\n",
    "# fixing data types\n",
    "cols = ['New cases', 'New deaths', 'New recovered']\n",
    "full_grouped[cols] = full_grouped[cols].astype('int')\n",
    "# \n",
    "full_grouped['New cases'] = full_grouped['New cases'].apply(lambda x: 0 if x<0 else x)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>2</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>Algeria</td>\n",
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       "      <th>3</th>\n",
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       "      <td>Andorra</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>Angola</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>22873</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>West Bank and Gaza</td>\n",
       "      <td>423</td>\n",
       "      <td>3</td>\n",
       "      <td>348.0</td>\n",
       "      <td>72.0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22874</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Western Sahara</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>6.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22875</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Yemen</td>\n",
       "      <td>212</td>\n",
       "      <td>39</td>\n",
       "      <td>0.0</td>\n",
       "      <td>173.0</td>\n",
       "      <td>3</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22876</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Zambia</td>\n",
       "      <td>920</td>\n",
       "      <td>7</td>\n",
       "      <td>336.0</td>\n",
       "      <td>577.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22877</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>Zimbabwe</td>\n",
       "      <td>56</td>\n",
       "      <td>4</td>\n",
       "      <td>18.0</td>\n",
       "      <td>34.0</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>22878 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Date      Country/Region  Confirmed  Deaths  Recovered  Active  \\\n",
       "0     2020-01-22         Afghanistan          0       0        0.0     0.0   \n",
       "1     2020-01-22             Albania          0       0        0.0     0.0   \n",
       "2     2020-01-22             Algeria          0       0        0.0     0.0   \n",
       "3     2020-01-22             Andorra          0       0        0.0     0.0   \n",
       "4     2020-01-22              Angola          0       0        0.0     0.0   \n",
       "...          ...                 ...        ...     ...        ...     ...   \n",
       "22873 2020-05-23  West Bank and Gaza        423       3      348.0    72.0   \n",
       "22874 2020-05-23      Western Sahara          6       0        6.0     0.0   \n",
       "22875 2020-05-23               Yemen        212      39        0.0   173.0   \n",
       "22876 2020-05-23              Zambia        920       7      336.0   577.0   \n",
       "22877 2020-05-23            Zimbabwe         56       4       18.0    34.0   \n",
       "\n",
       "       New cases  New deaths  New recovered  \n",
       "0              0           0              0  \n",
       "1              0           0              0  \n",
       "2              0           0              0  \n",
       "3              0           0              0  \n",
       "4              0           0              0  \n",
       "...          ...         ...            ...  \n",
       "22873          0           1              2  \n",
       "22874          0           0              0  \n",
       "22875          3           6              0  \n",
       "22876          0           0              0  \n",
       "22877          5           0              0  \n",
       "\n",
       "[22878 rows x 9 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Save cleaned data to a local .csv file\n",
    "full_grouped.to_csv('COVID-19-time-series-clean-complete.csv', index = False)\n",
    "full_grouped"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Make Interactive Line Plot with DateSlider"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "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>Date</th>\n",
       "      <th>Country/Region</th>\n",
       "      <th>Confirmed</th>\n",
       "      <th>Deaths</th>\n",
       "      <th>Recovered</th>\n",
       "      <th>Active</th>\n",
       "      <th>New cases</th>\n",
       "      <th>New deaths</th>\n",
       "      <th>New recovered</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>172</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>US</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>358</th>\n",
       "      <td>2020-01-23</td>\n",
       "      <td>US</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>544</th>\n",
       "      <td>2020-01-24</td>\n",
       "      <td>US</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>730</th>\n",
       "      <td>2020-01-25</td>\n",
       "      <td>US</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>916</th>\n",
       "      <td>2020-01-26</td>\n",
       "      <td>US</td>\n",
       "      <td>5</td>\n",
       "      <td>0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.0</td>\n",
       "      <td>3</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22120</th>\n",
       "      <td>2020-05-19</td>\n",
       "      <td>US</td>\n",
       "      <td>1528568</td>\n",
       "      <td>91921</td>\n",
       "      <td>289392.0</td>\n",
       "      <td>1147255.0</td>\n",
       "      <td>20260</td>\n",
       "      <td>1574</td>\n",
       "      <td>6214</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22306</th>\n",
       "      <td>2020-05-20</td>\n",
       "      <td>US</td>\n",
       "      <td>1551853</td>\n",
       "      <td>93439</td>\n",
       "      <td>294312.0</td>\n",
       "      <td>1164102.0</td>\n",
       "      <td>23285</td>\n",
       "      <td>1518</td>\n",
       "      <td>4920</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22492</th>\n",
       "      <td>2020-05-21</td>\n",
       "      <td>US</td>\n",
       "      <td>1577147</td>\n",
       "      <td>94702</td>\n",
       "      <td>298418.0</td>\n",
       "      <td>1184027.0</td>\n",
       "      <td>25294</td>\n",
       "      <td>1263</td>\n",
       "      <td>4106</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22678</th>\n",
       "      <td>2020-05-22</td>\n",
       "      <td>US</td>\n",
       "      <td>1600937</td>\n",
       "      <td>95979</td>\n",
       "      <td>350135.0</td>\n",
       "      <td>1154823.0</td>\n",
       "      <td>23790</td>\n",
       "      <td>1277</td>\n",
       "      <td>51717</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22864</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>US</td>\n",
       "      <td>1622612</td>\n",
       "      <td>97087</td>\n",
       "      <td>361239.0</td>\n",
       "      <td>1164286.0</td>\n",
       "      <td>21675</td>\n",
       "      <td>1108</td>\n",
       "      <td>11104</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>123 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Date Country/Region  Confirmed  Deaths  Recovered     Active  \\\n",
       "172   2020-01-22             US          1       0        0.0        1.0   \n",
       "358   2020-01-23             US          1       0        0.0        1.0   \n",
       "544   2020-01-24             US          2       0        0.0        2.0   \n",
       "730   2020-01-25             US          2       0        0.0        2.0   \n",
       "916   2020-01-26             US          5       0        0.0        5.0   \n",
       "...          ...            ...        ...     ...        ...        ...   \n",
       "22120 2020-05-19             US    1528568   91921   289392.0  1147255.0   \n",
       "22306 2020-05-20             US    1551853   93439   294312.0  1164102.0   \n",
       "22492 2020-05-21             US    1577147   94702   298418.0  1184027.0   \n",
       "22678 2020-05-22             US    1600937   95979   350135.0  1154823.0   \n",
       "22864 2020-05-23             US    1622612   97087   361239.0  1164286.0   \n",
       "\n",
       "       New cases  New deaths  New recovered  \n",
       "172            0           0              0  \n",
       "358            0           0              0  \n",
       "544            1           0              0  \n",
       "730            0           0              0  \n",
       "916            3           0              0  \n",
       "...          ...         ...            ...  \n",
       "22120      20260        1574           6214  \n",
       "22306      23285        1518           4920  \n",
       "22492      25294        1263           4106  \n",
       "22678      23790        1277          51717  \n",
       "22864      21675        1108          11104  \n",
       "\n",
       "[123 rows x 9 columns]"
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_country = full_grouped[full_grouped['Country/Region'] == 'US']\n",
    "df_country"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "    <div class=\"bk-root\">\n",
       "        <a href=\"https://bokeh.org\" target=\"_blank\" class=\"bk-logo bk-logo-small bk-logo-notebook\"></a>\n",
       "        <span id=\"1001\">Loading BokehJS ...</span>\n",
       "    </div>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "application/javascript": [
       "\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",
       "  var JS_MIME_TYPE = 'application/javascript';\n",
       "  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",
       "        toinsert[toinsert.length - 1].firstChild.textContent = bk_div.children[0].textContent\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",
       "    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.1.min.js\": \"JpP8FXbgAZLkfur7LiK3j9AGBhHNIvF742meBJrjO2ShJDhCG2I1uVvW+0DUtrmc\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.1.min.js\": \"xZlADit0Q04ISQEdKg2k3L4W9AwQBAuDs9nJL9fM/WwzL1tEU9VPNezOFX0nLEAz\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.1.min.js\": \"4BuPRZkdMKSnj3zoxiNrQ86XgNw0rYmBOxe7nshquXwwcauupgBF2DHLVG1WuZlV\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.1.min.js\": \"Dv1SQ87hmDqK6S5OhBf0bCuwAEvL5QYL0PuR/F1SPVhCS/r/abjkbpKDYL2zeM19\"};\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",
       "      if (url in hashes) {\n",
       "        element.crossOrigin = \"anonymous\";\n",
       "        element.integrity = \"sha384-\" + hashes[url];\n",
       "      }\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.bokeh.org/bokeh/release/bokeh-2.0.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.1.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    const hashes = {\"https://cdn.bokeh.org/bokeh/release/bokeh-2.0.1.min.js\": \"JpP8FXbgAZLkfur7LiK3j9AGBhHNIvF742meBJrjO2ShJDhCG2I1uVvW+0DUtrmc\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.1.min.js\": \"xZlADit0Q04ISQEdKg2k3L4W9AwQBAuDs9nJL9fM/WwzL1tEU9VPNezOFX0nLEAz\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.1.min.js\": \"4BuPRZkdMKSnj3zoxiNrQ86XgNw0rYmBOxe7nshquXwwcauupgBF2DHLVG1WuZlV\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.1.min.js\": \"Dv1SQ87hmDqK6S5OhBf0bCuwAEvL5QYL0PuR/F1SPVhCS/r/abjkbpKDYL2zeM19\"};\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      if (url in hashes) {\n        element.crossOrigin = \"anonymous\";\n        element.integrity = \"sha384-\" + hashes[url];\n      }\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.bokeh.org/bokeh/release/bokeh-2.0.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-2.0.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-2.0.1.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-2.0.1.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"
    }
   ],
   "source": [
    "import time\n",
    "from datetime import datetime\n",
    "\n",
    "import pandas as pd\n",
    "from bokeh.layouts import column\n",
    "from bokeh.models import ColumnDataSource, Slider, DateSlider,  HoverTool, Range1d\n",
    "from bokeh.plotting import figure\n",
    "from bokeh.themes import Theme\n",
    "from bokeh.io import show, output_notebook\n",
    "\n",
    "output_notebook()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "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>Date</th>\n",
       "      <th>Confirmed</th>\n",
       "      <th>Deaths</th>\n",
       "      <th>Recovered</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>2020-01-22</td>\n",
       "      <td>555</td>\n",
       "      <td>17</td>\n",
       "      <td>28.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>2020-01-23</td>\n",
       "      <td>654</td>\n",
       "      <td>18</td>\n",
       "      <td>30.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2020-01-24</td>\n",
       "      <td>941</td>\n",
       "      <td>26</td>\n",
       "      <td>35.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>2020-01-25</td>\n",
       "      <td>1434</td>\n",
       "      <td>42</td>\n",
       "      <td>38.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>2020-01-26</td>\n",
       "      <td>2118</td>\n",
       "      <td>56</td>\n",
       "      <td>51.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>118</th>\n",
       "      <td>2020-05-19</td>\n",
       "      <td>4896757</td>\n",
       "      <td>323269</td>\n",
       "      <td>1787190.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>119</th>\n",
       "      <td>2020-05-20</td>\n",
       "      <td>4995737</td>\n",
       "      <td>328099</td>\n",
       "      <td>1844969.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>120</th>\n",
       "      <td>2020-05-21</td>\n",
       "      <td>5101689</td>\n",
       "      <td>332908</td>\n",
       "      <td>1894995.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>121</th>\n",
       "      <td>2020-05-22</td>\n",
       "      <td>5210082</td>\n",
       "      <td>338144</td>\n",
       "      <td>2001275.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>122</th>\n",
       "      <td>2020-05-23</td>\n",
       "      <td>5309627</td>\n",
       "      <td>342081</td>\n",
       "      <td>2055954.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>123 rows × 4 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          Date  Confirmed  Deaths  Recovered\n",
       "0   2020-01-22        555      17       28.0\n",
       "1   2020-01-23        654      18       30.0\n",
       "2   2020-01-24        941      26       35.0\n",
       "3   2020-01-25       1434      42       38.0\n",
       "4   2020-01-26       2118      56       51.0\n",
       "..         ...        ...     ...        ...\n",
       "118 2020-05-19    4896757  323269  1787190.0\n",
       "119 2020-05-20    4995737  328099  1844969.0\n",
       "120 2020-05-21    5101689  332908  1894995.0\n",
       "121 2020-05-22    5210082  338144  2001275.0\n",
       "122 2020-05-23    5309627  342081  2055954.0\n",
       "\n",
       "[123 rows x 4 columns]"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "## Group by date and aggregate\n",
    "global_count_df = full_grouped.groupby(['Date'])[['Confirmed', 'Deaths', 'Recovered']]\n",
    "global_count_df = global_count_df.sum().reset_index()\n",
    "global_count_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Global COVID Spread FROM: 22-01-2020 TO: 23-05-2020\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Confirmed</th>\n",
       "      <th>Deaths</th>\n",
       "      <th>Recovered</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Date</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>2020-01-22</th>\n",
       "      <td>555</td>\n",
       "      <td>17</td>\n",
       "      <td>28.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-23</th>\n",
       "      <td>654</td>\n",
       "      <td>18</td>\n",
       "      <td>30.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-24</th>\n",
       "      <td>941</td>\n",
       "      <td>26</td>\n",
       "      <td>35.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-25</th>\n",
       "      <td>1434</td>\n",
       "      <td>42</td>\n",
       "      <td>38.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-26</th>\n",
       "      <td>2118</td>\n",
       "      <td>56</td>\n",
       "      <td>51.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-05-19</th>\n",
       "      <td>4896757</td>\n",
       "      <td>323269</td>\n",
       "      <td>1787190.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-05-20</th>\n",
       "      <td>4995737</td>\n",
       "      <td>328099</td>\n",
       "      <td>1844969.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-05-21</th>\n",
       "      <td>5101689</td>\n",
       "      <td>332908</td>\n",
       "      <td>1894995.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-05-22</th>\n",
       "      <td>5210082</td>\n",
       "      <td>338144</td>\n",
       "      <td>2001275.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-05-23</th>\n",
       "      <td>5309627</td>\n",
       "      <td>342081</td>\n",
       "      <td>2055954.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>123 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            Confirmed  Deaths  Recovered\n",
       "Date                                    \n",
       "2020-01-22        555      17       28.0\n",
       "2020-01-23        654      18       30.0\n",
       "2020-01-24        941      26       35.0\n",
       "2020-01-25       1434      42       38.0\n",
       "2020-01-26       2118      56       51.0\n",
       "...               ...     ...        ...\n",
       "2020-05-19    4896757  323269  1787190.0\n",
       "2020-05-20    4995737  328099  1844969.0\n",
       "2020-05-21    5101689  332908  1894995.0\n",
       "2020-05-22    5210082  338144  2001275.0\n",
       "2020-05-23    5309627  342081  2055954.0\n",
       "\n",
       "[123 rows x 3 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# global_count_df['Date'] =  global_count_df['Date'].dt.strftime('%d-%m-%Y')\n",
    "global_count_df['Date'] = pd.to_datetime(global_count_df['Date'],dayfirst = True)\n",
    "# global_count_df['Date'] = global_count_df['Date'].astype('datetime64[D]')\n",
    "first_date = global_count_df['Date'][0]\n",
    "last_date = global_count_df['Date'][len(global_count_df)-1]\n",
    "global_count_df.set_index('Date', drop = True, inplace = True)\n",
    "print('Global COVID Spread FROM:',first_date.strftime('%d-%m-%Y'),'TO:',last_date.strftime('%d-%m-%Y'))\n",
    "global_count_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "        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>Confirmed</th>\n",
       "      <th>Deaths</th>\n",
       "      <th>Recovered</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Date</th>\n",
       "      <th></th>\n",
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       "  <tbody>\n",
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       "      <th>2020-01-22</th>\n",
       "      <td>555</td>\n",
       "      <td>17</td>\n",
       "      <td>28.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-23</th>\n",
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       "      <th>2020-01-24</th>\n",
       "      <td>941</td>\n",
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       "    </tr>\n",
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       "      <th>2020-01-25</th>\n",
       "      <td>1434</td>\n",
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       "      <td>51.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-27</th>\n",
       "      <td>2927</td>\n",
       "      <td>82</td>\n",
       "      <td>58.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-28</th>\n",
       "      <td>5578</td>\n",
       "      <td>131</td>\n",
       "      <td>103.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-29</th>\n",
       "      <td>6166</td>\n",
       "      <td>133</td>\n",
       "      <td>120.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-30</th>\n",
       "      <td>8234</td>\n",
       "      <td>171</td>\n",
       "      <td>136.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2020-01-31</th>\n",
       "      <td>9927</td>\n",
       "      <td>213</td>\n",
       "      <td>209.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            Confirmed  Deaths  Recovered\n",
       "Date                                    \n",
       "2020-01-22        555      17       28.0\n",
       "2020-01-23        654      18       30.0\n",
       "2020-01-24        941      26       35.0\n",
       "2020-01-25       1434      42       38.0\n",
       "2020-01-26       2118      56       51.0\n",
       "2020-01-27       2927      82       58.0\n",
       "2020-01-28       5578     131      103.0\n",
       "2020-01-29       6166     133      120.0\n",
       "2020-01-30       8234     171      136.0\n",
       "2020-01-31       9927     213      209.0"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Restrict data by date\n",
    "global_count_df.loc[:'31-01-2020']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "def bokeh_app(doc):\n",
    "    df = global_count_df.copy()\n",
    "    source = ColumnDataSource(data=df)\n",
    "#     HoverTool(tooltips=[(\"Date\", \"@ENTRYDATE{%F}\"), (\"Transactions\", \"@Transactions\")], formatters={\"@ENTRYDATE\":\"datetime\"}, mode='vline')\n",
    "    hover = HoverTool(names=['covidcount'],tooltips=[(\"Date\", \"$x{%d-%m-%Y}\"),(\"Count\", \"$y{0,000,000}\")],formatters={\"$x\": \"datetime\"}, mode='mouse')\n",
    "    hover.point_policy= \"snap_to_data\"\n",
    "    plot = figure(title=\"@Dilip Rajkumar - Global COVID-19 Historic Spread - Bokeh Visualization\",\n",
    "                 plot_width=1200, plot_height=540, x_axis_type='datetime', y_axis_label='Nr. of Cases')\n",
    "#     plot.x_range=DataRange1d(bounds=(None, 120))\n",
    "    plot.x_range=Range1d(first_date, last_date)\n",
    "    plot.y_range=Range1d(10, global_count_df['Confirmed'].max()*1.10)\n",
    "    plot.add_tools(hover)\n",
    "    plot.line('Date', 'Confirmed', source=source, color = 'orange',line_width=2, name = 'covidcount', legend_label=\"Nr. of ConfirmedCases\", )\n",
    "    plot.line('Date', 'Deaths', source=source, color = 'red',line_width=2,name = 'covidcount', legend_label=\"Nr. of Deaths\")\n",
    "    plot.line('Date', 'Recovered', source=source, color = 'green',line_width=2,name = 'covidcount', legend_label=\"Nr. of Recovered Cases\")\n",
    "    plot.legend.location = 'top_left'\n",
    "    \n",
    "    def callback(attr, old, new):\n",
    "        date_value =  slider.value\n",
    "        last_date = datetime.fromtimestamp(date_value/1000).strftime('%d-%m-%Y')\n",
    "        df_trunc = df.loc[: last_date]\n",
    "        source.data = df_trunc  \n",
    "\n",
    "    slider = DateSlider(start=first_date, end=last_date, value='31-01-2020', step=1, title=\"Date\")\n",
    "    slider.on_change('value', callback)\n",
    "\n",
    "    doc.add_root(column(slider, plot))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.bokehjs_exec.v0+json": "",
      "text/html": [
       "\n",
       "<script id=\"1002\">\n",
       "  var xhr = new XMLHttpRequest()\n",
       "  xhr.responseType = 'blob';\n",
       "  xhr.open('GET', \"http://localhost:53698/autoload.js?bokeh-autoload-element=1002&bokeh-absolute-url=http://localhost:53698&resources=none\", true);\n",
       "  \n",
       "  xhr.onload = function (event) {\n",
       "    var script = document.createElement('script'),\n",
       "    src = URL.createObjectURL(event.target.response);\n",
       "    script.src = src;\n",
       "    document.body.appendChild(script);\n",
       "  };\n",
       "xhr.send();\n",
       "</script>"
      ]
     },
     "metadata": {
      "application/vnd.bokehjs_exec.v0+json": {
       "server_id": "a79fcfbf6368419da1fe079554652949"
      }
     },
     "output_type": "display_data"
    }
   ],
   "source": [
    "show(bokeh_app)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### References:\n",
    "1. [COVID 19 - Data Wrangling and Cleaning](https://towardsdatascience.com/covid-19-data-processing-58aaa3663f6)\n",
    "2. [Bokeh AAPL Stocks - DateTime formatting](http://docs.bokeh.org/en/1.0.2/docs/user_guide/examples/tools_hover_tooltip_formatting.html)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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