{
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"source": [
"import numpy as np\n",
"import pandas as pd\n",
"\n",
"from bokeh.charts import Histogram, Bar, BoxPlot\n",
"from bokeh.plotting import figure, show\n",
"from bokeh.io import output_notebook"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Ebola outbreaks data before 2014"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"ebola_df = pd.read_csv(\"data/out/ebola_outbreaks_before_2014-geometry_fixed.csv\", encoding=\"utf-8\", index_col=False)\n",
"\n",
"ebola_data = ebola_df.drop(ebola_df.columns[[0, 1, 2, 9]], axis=1)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Data set description"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"column 1 : country_code_iso_2_digits\n",
"column 2 : country_name\n",
"column 3 : duration_days\n",
"column 4 : ebola_subtype\n",
"column 5 : end_date\n",
"column 6 : end_datetime\n",
"column 7 : geometry\n",
"column 8 : geometry_geojson\n",
"column 9 : latitude\n",
"column 10 : longitude\n",
"column 11 : reported_number_of_deaths_among_cases\n",
"column 12 : reported_number_of_human_cases\n",
"column 13 : reported_of_deaths_among_cases\n",
"column 14 : start_date\n",
"column 15 : start_datetime\n",
"column 16 : year_s\n"
]
}
],
"source": [
"cols = list(ebola_data.columns)\n",
"\n",
"for column in cols:\n",
" print \"column\", (cols.index(column) + 1), \":\", column"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"**=> locations info, reported cases, date/time**"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Number of outbreaks per countries"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false,
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"country_name\n",
"Côte d'Ivoire (Ivory Coast) 1\n",
"England 1\n",
"Italy 1\n",
"South Africa 1\n",
"Russia 2\n",
"Philippines 3\n",
"Sudan (South Sudan) 3\n",
"USA 3\n",
"Gabon 4\n",
"Uganda 5\n",
"Democratic Republic of the Congo 9\n",
"Name: country_name, dtype: int64"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ebola_data.groupby([\"country_name\"])[\"country_name\"].count().order()"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"# Bokeh can't seem to handle the unicode for circumflex accent on the 'o' in \"Côte d'Ivoire\"\n",
"# I'm replacing it by a normal 'o'\n",
"\n",
"countries_list = list(ebola_data[\"country_name\"])\n",
"\n",
"for i in range(len(countries_list)): \n",
" if countries_list[i] == u\"C\\xf4te d'Ivoire (Ivory Coast)\":\n",
" countries_list[i] = u\"Cote d'Ivoire (Ivory Coast)\""
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
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"data_nb = {\n",
" 'countries': countries_list,\n",
" 'ebola outbreaks': [1] * len(countries_list)\n",
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"bar_nb = Bar(data_nb, values='ebola outbreaks', label='countries', agg='sum', color=\"#3B6849\",\n",
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"source": [
"### The average number of days for an outbreak per country"
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"country_name\n",
"Uganda 206.800000\n",
"Gabon 219.750000\n",
"Democratic Republic of the Congo 235.444444\n",
"Côte d'Ivoire (Ivory Coast) 364.000000\n",
"USA 364.333333\n",
"Philippines 364.666667\n",
"Sudan (South Sudan) 364.666667\n",
"England 365.000000\n",
"Italy 365.000000\n",
"Russia 365.000000\n",
"South Africa 365.000000\n",
"Name: duration_days, dtype: float64"
]
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"source": [
"ebola_data.groupby([\"country_name\"])[\"duration_days\"].mean().order()"
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"source": [
"data_dur = {\n",
" 'countries': countries_list,\n",
" 'outbreaks duration': list(ebola_data[\"duration_days\"])\n",
"}\n",
"\n",
"bar_dur = Bar(data_dur, values='outbreaks duration', label='countries', agg='mean', color=\"#586996\",\n",
" title=\"Durations of ebola outbreaks (days) per country\", plot_width=600, plot_height=500)\n",
"\n",
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"source": [
"### Ebola virus subtypes"
]
},
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"cell_type": "code",
"execution_count": 9,
"metadata": {
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"outputs": [
{
"data": {
"text/plain": [
"ebola_subtype\n",
"Taï Forest virus 1\n",
"Bundibugyo virus 2\n",
"Reston virus 7\n",
"Sudan virus 8\n",
"Zaire virus 15\n",
"Name: ebola_subtype, dtype: int64"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
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],
"source": [
"ebola_data.groupby([\"ebola_subtype\"])[\"ebola_subtype\"].count().order()"
]
},
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"cell_type": "code",
"execution_count": 10,
"metadata": {
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"source": [
"# Bokeh can't seem to handle the unicode for trema accent on the 'i' in Taï Forest virus\n",
"# I'm replacing it by a normal 'i'\n",
"\n",
"eb_virus_types = list(ebola_data[\"ebola_subtype\"])\n",
"\n",
"for i in range(len(eb_virus_types)): \n",
" if eb_virus_types[i] == u\"Ta\\xef Forest virus\":\n",
" eb_virus_types[i] = u\"Tai Forest virus\""
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
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"<p><code><Bokeh Notebook handle for <strong>In[11]</strong>></code></p>"
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"data_vir = {\n",
" 'ebola virus subtypes': eb_virus_types,\n",
" 'number of ebola outbreaks': [1] * len(eb_virus_types)\n",
"}\n",
"\n",
"bar_vir = Bar(data_vir, values='number of ebola outbreaks', label='ebola virus subtypes', agg='sum', color=\"#E2AE7A\",\n",
" title=\"Number of ebola outbreak(s) per virus subtype\", plot_width=600, plot_height=400, bar_width=0.5)\n",
"\n",
"output_notebook()\n",
"\n",
"show(bar_vir)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
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{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>country_name</th>\n",
" <th>ebola_subtype</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>30</th>\n",
" <td>Côte d'Ivoire (Ivory Coast)</td>\n",
" <td>Taï Forest virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Bundibugyo virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>Democratic Republic of the Congo</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>32</th>\n",
" <td>England</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>13</th>\n",
" <td>Gabon</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>Gabon</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>20</th>\n",
" <td>Gabon</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>23</th>\n",
" <td>Gabon</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>24</th>\n",
" <td>Italy</td>\n",
" <td>Reston virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>7</th>\n",
" <td>Philippines</td>\n",
" <td>Reston virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>14</th>\n",
" <td>Philippines</td>\n",
" <td>Reston virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>Philippines</td>\n",
" <td>Reston virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>Russia</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>19</th>\n",
" <td>Russia</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>27</th>\n",
" <td>South Africa</td>\n",
" <td>Zaire virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>31</th>\n",
" <td>Sudan (South Sudan)</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>29</th>\n",
" <td>Sudan (South Sudan)</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>28</th>\n",
" <td>Sudan (South Sudan)</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>21</th>\n",
" <td>USA</td>\n",
" <td>Reston virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>USA</td>\n",
" <td>Reston virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>USA</td>\n",
" <td>Reston virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>26</th>\n",
" <td>Uganda</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>22</th>\n",
" <td>Uganda</td>\n",
" <td>Bundibugyo virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>9</th>\n",
" <td>Uganda</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25</th>\n",
" <td>Uganda</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" <tr>\n",
" <th>11</th>\n",
" <td>Uganda</td>\n",
" <td>Sudan virus</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" country_name ebola_subtype\n",
"30 Côte d'Ivoire (Ivory Coast) Taï Forest virus\n",
"16 Democratic Republic of the Congo Zaire virus\n",
"18 Democratic Republic of the Congo Zaire virus\n",
"17 Democratic Republic of the Congo Zaire virus\n",
"15 Democratic Republic of the Congo Bundibugyo virus\n",
"5 Democratic Republic of the Congo Zaire virus\n",
"6 Democratic Republic of the Congo Zaire virus\n",
"12 Democratic Republic of the Congo Zaire virus\n",
"8 Democratic Republic of the Congo Zaire virus\n",
"10 Democratic Republic of the Congo Zaire virus\n",
"32 England Sudan virus\n",
"13 Gabon Zaire virus\n",
"4 Gabon Zaire virus\n",
"20 Gabon Zaire virus\n",
"23 Gabon Zaire virus\n",
"24 Italy Reston virus\n",
"7 Philippines Reston virus\n",
"14 Philippines Reston virus\n",
"1 Philippines Reston virus\n",
"0 Russia Zaire virus\n",
"19 Russia Zaire virus\n",
"27 South Africa Zaire virus\n",
"31 Sudan (South Sudan) Sudan virus\n",
"29 Sudan (South Sudan) Sudan virus\n",
"28 Sudan (South Sudan) Sudan virus\n",
"21 USA Reston virus\n",
"2 USA Reston virus\n",
"3 USA Reston virus\n",
"26 Uganda Sudan virus\n",
"22 Uganda Bundibugyo virus\n",
"9 Uganda Sudan virus\n",
"25 Uganda Sudan virus\n",
"11 Uganda Sudan virus"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ebola_data[[\"country_name\", \"ebola_subtype\"]].sort([\"country_name\"])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Duration of epidemy in days by virus subtype"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"ebola_subtype\n",
"Bundibugyo virus 121.500000\n",
"Zaire virus 260.733333\n",
"Sudan virus 304.000000\n",
"Taï Forest virus 364.000000\n",
"Reston virus 364.571429\n",
"Name: duration_days, dtype: float64"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ebola_data.groupby([\"ebola_subtype\"])[\"duration_days\"].mean().order()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"__=> Bundibugyo virus seems to be correlated with shorter outbreaks__"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Human cases for DRC (country with the most cases)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>ebola_subtype</th>\n",
" <th>start_date</th>\n",
" <th>end_date</th>\n",
" <th>reported_number_of_human_cases</th>\n",
" <th>reported_number_of_deaths_among_cases</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>5</th>\n",
" <td>Zaire virus</td>\n",
" <td>1976-01-01T00:00:00Z</td>\n",
" <td>1976-12-31T00:00:00Z</td>\n",
" <td>318</td>\n",
" <td>280</td>\n",
" </tr>\n",
" <tr>\n",
" <th>8</th>\n",
" <td>Zaire virus</td>\n",
" <td>1977-01-01T00:00:00Z</td>\n",
" <td>1977-12-31T00:00:00Z</td>\n",
" <td>1</td>\n",
" <td>1</td>\n",
" </tr>\n",
" <tr>\n",
" <th>18</th>\n",
" <td>Zaire virus</td>\n",
" <td>1995-01-01T00:00:00Z</td>\n",
" <td>1995-12-31T00:00:00Z</td>\n",
" <td>315</td>\n",
" <td>250</td>\n",
" </tr>\n",
" <tr>\n",
" <th>16</th>\n",
" <td>Zaire virus</td>\n",
" <td>2001-10-01T00:00:00Z</td>\n",
" <td>2002-03-31T00:00:00Z</td>\n",
" <td>57</td>\n",
" <td>43</td>\n",
" </tr>\n",
" <tr>\n",
" <th>17</th>\n",
" <td>Zaire virus</td>\n",
" <td>2002-12-01T00:00:00Z</td>\n",
" <td>2003-04-30T00:00:00Z</td>\n",
" <td>143</td>\n",
" <td>128</td>\n",
" </tr>\n",
" <tr>\n",
" <th>10</th>\n",
" <td>Zaire virus</td>\n",
" <td>2003-11-01T00:00:00Z</td>\n",
" <td>2003-12-31T00:00:00Z</td>\n",
" <td>35</td>\n",
" <td>29</td>\n",
" </tr>\n",
" <tr>\n",
" <th>6</th>\n",
" <td>Zaire virus</td>\n",
" <td>2007-01-01T00:00:00Z</td>\n",
" <td>2007-12-31T00:00:00Z</td>\n",
" <td>264</td>\n",
" <td>187</td>\n",
" </tr>\n",
" <tr>\n",
" <th>12</th>\n",
" <td>Zaire virus</td>\n",
" <td>2008-12-01T00:00:00Z</td>\n",
" <td>2009-02-28T00:00:00Z</td>\n",
" <td>32</td>\n",
" <td>15</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15</th>\n",
" <td>Bundibugyo virus</td>\n",
" <td>2012-06-01T00:00:00Z</td>\n",
" <td>2012-11-30T00:00:00Z</td>\n",
" <td>36</td>\n",
" <td>13</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" ebola_subtype start_date end_date \\\n",
"5 Zaire virus 1976-01-01T00:00:00Z 1976-12-31T00:00:00Z \n",
"8 Zaire virus 1977-01-01T00:00:00Z 1977-12-31T00:00:00Z \n",
"18 Zaire virus 1995-01-01T00:00:00Z 1995-12-31T00:00:00Z \n",
"16 Zaire virus 2001-10-01T00:00:00Z 2002-03-31T00:00:00Z \n",
"17 Zaire virus 2002-12-01T00:00:00Z 2003-04-30T00:00:00Z \n",
"10 Zaire virus 2003-11-01T00:00:00Z 2003-12-31T00:00:00Z \n",
"6 Zaire virus 2007-01-01T00:00:00Z 2007-12-31T00:00:00Z \n",
"12 Zaire virus 2008-12-01T00:00:00Z 2009-02-28T00:00:00Z \n",
"15 Bundibugyo virus 2012-06-01T00:00:00Z 2012-11-30T00:00:00Z \n",
"\n",
" reported_number_of_human_cases reported_number_of_deaths_among_cases \n",
"5 318 280 \n",
"8 1 1 \n",
"18 315 250 \n",
"16 57 43 \n",
"17 143 128 \n",
"10 35 29 \n",
"6 264 187 \n",
"12 32 15 \n",
"15 36 13 "
]
},
"execution_count": 14,
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],
"source": [
"df_drc = ebola_data[ebola_data.country_name == \"Democratic Republic of the Congo\"]\n",
"\n",
"drc = df_drc[[\"ebola_subtype\", \"start_date\", \"end_date\", \"reported_number_of_human_cases\", \"reported_number_of_deaths_among_cases\"]]\n",
"\n",
"drc.sort([\"start_date\"])"
]
}
],
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