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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"import requests\n",
"import io\n",
"import plotly.express as px"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"data_url = \"https://data.cdc.gov/api/views/vsak-wrfu/rows.csv?accessType=DOWNLOAD\""
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"req = requests.get(data_url)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"b'Data as of,State,MMWR Week,Week ending Date,Sex,Age Group,Total Deaths,COVID-19 Deaths\\n07/01/2020,Un'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"req.content[0:100]"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"raw_df = pd.read_csv(io.StringIO(req.content.decode('utf-8')))"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
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" vertical-align: top;\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>Data as of</th>\n",
" <th>State</th>\n",
" <th>MMWR Week</th>\n",
" <th>Week ending Date</th>\n",
" <th>Sex</th>\n",
" <th>Age Group</th>\n",
" <th>Total Deaths</th>\n",
" <th>COVID-19 Deaths</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>5</td>\n",
" <td>02/01/2020</td>\n",
" <td>Female</td>\n",
" <td>Under 1 year</td>\n",
" <td>185</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>5</td>\n",
" <td>02/01/2020</td>\n",
" <td>Female</td>\n",
" <td>1-4 years</td>\n",
" <td>28</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>5</td>\n",
" <td>02/01/2020</td>\n",
" <td>Female</td>\n",
" <td>5-14 years</td>\n",
" <td>48</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>5</td>\n",
" <td>02/01/2020</td>\n",
" <td>Female</td>\n",
" <td>15-24 years</td>\n",
" <td>146</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>5</td>\n",
" <td>02/01/2020</td>\n",
" <td>Female</td>\n",
" <td>25-34 years</td>\n",
" <td>328</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",
" </tr>\n",
" <tr>\n",
" <th>721</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>45-54 years</td>\n",
" <td>761</td>\n",
" <td>18</td>\n",
" </tr>\n",
" <tr>\n",
" <th>722</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>55-64 years</td>\n",
" <td>1875</td>\n",
" <td>32</td>\n",
" </tr>\n",
" <tr>\n",
" <th>723</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>65-74 years</td>\n",
" <td>3024</td>\n",
" <td>45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>724</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>75-84 years</td>\n",
" <td>4190</td>\n",
" <td>53</td>\n",
" </tr>\n",
" <tr>\n",
" <th>725</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>85 years and over</td>\n",
" <td>5703</td>\n",
" <td>78</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>726 rows × 8 columns</p>\n",
"</div>"
],
"text/plain": [
" Data as of State MMWR Week Week ending Date Sex \\\n",
"0 07/01/2020 United States 5 02/01/2020 Female \n",
"1 07/01/2020 United States 5 02/01/2020 Female \n",
"2 07/01/2020 United States 5 02/01/2020 Female \n",
"3 07/01/2020 United States 5 02/01/2020 Female \n",
"4 07/01/2020 United States 5 02/01/2020 Female \n",
".. ... ... ... ... ... \n",
"721 07/01/2020 United States 26 06/27/2020 All Sex \n",
"722 07/01/2020 United States 26 06/27/2020 All Sex \n",
"723 07/01/2020 United States 26 06/27/2020 All Sex \n",
"724 07/01/2020 United States 26 06/27/2020 All Sex \n",
"725 07/01/2020 United States 26 06/27/2020 All Sex \n",
"\n",
" Age Group Total Deaths COVID-19 Deaths \n",
"0 Under 1 year 185 0 \n",
"1 1-4 years 28 0 \n",
"2 5-14 years 48 0 \n",
"3 15-24 years 146 0 \n",
"4 25-34 years 328 0 \n",
".. ... ... ... \n",
"721 45-54 years 761 18 \n",
"722 55-64 years 1875 32 \n",
"723 65-74 years 3024 45 \n",
"724 75-84 years 4190 53 \n",
"725 85 years and over 5703 78 \n",
"\n",
"[726 rows x 8 columns]"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"raw_df"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"all_sex_df = raw_df[raw_df.Sex == \"All Sex\"]"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
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" <th>487</th>\n",
" <td>07/01/2020</td>\n",
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" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
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" <td>3024</td>\n",
" <td>45</td>\n",
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"</div>"
],
"text/plain": [
" Data as of State MMWR Week Week ending Date Sex \\\n",
"484 07/01/2020 United States 5 02/01/2020 All Sex \n",
"485 07/01/2020 United States 5 02/01/2020 All Sex \n",
"486 07/01/2020 United States 5 02/01/2020 All Sex \n",
"487 07/01/2020 United States 5 02/01/2020 All Sex \n",
"488 07/01/2020 United States 5 02/01/2020 All Sex \n",
".. ... ... ... ... ... \n",
"721 07/01/2020 United States 26 06/27/2020 All Sex \n",
"722 07/01/2020 United States 26 06/27/2020 All Sex \n",
"723 07/01/2020 United States 26 06/27/2020 All Sex \n",
"724 07/01/2020 United States 26 06/27/2020 All Sex \n",
"725 07/01/2020 United States 26 06/27/2020 All Sex \n",
"\n",
" Age Group Total Deaths COVID-19 Deaths \n",
"484 Under 1 year 375 0 \n",
"485 1-4 years 64 0 \n",
"486 5-14 years 110 0 \n",
"487 15-24 years 567 0 \n",
"488 25-34 years 1124 0 \n",
".. ... ... ... \n",
"721 45-54 years 761 18 \n",
"722 55-64 years 1875 32 \n",
"723 65-74 years 3024 45 \n",
"724 75-84 years 4190 53 \n",
"725 85 years and over 5703 78 \n",
"\n",
"[242 rows x 8 columns]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"all_sex_df"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"whole_us_df = all_sex_df[all_sex_df.State == \"United States\"]"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
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" <tr>\n",
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" <td>761</td>\n",
" <td>18</td>\n",
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" <tr>\n",
" <th>723</th>\n",
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" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>65-74 years</td>\n",
" <td>3024</td>\n",
" <td>45</td>\n",
" </tr>\n",
" <tr>\n",
" <th>724</th>\n",
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" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>75-84 years</td>\n",
" <td>4190</td>\n",
" <td>53</td>\n",
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" <tr>\n",
" <th>725</th>\n",
" <td>07/01/2020</td>\n",
" <td>United States</td>\n",
" <td>26</td>\n",
" <td>06/27/2020</td>\n",
" <td>All Sex</td>\n",
" <td>85 years and over</td>\n",
" <td>5703</td>\n",
" <td>78</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"<p>242 rows × 8 columns</p>\n",
"</div>"
],
"text/plain": [
" Data as of State MMWR Week Week ending Date Sex \\\n",
"484 07/01/2020 United States 5 02/01/2020 All Sex \n",
"485 07/01/2020 United States 5 02/01/2020 All Sex \n",
"486 07/01/2020 United States 5 02/01/2020 All Sex \n",
"487 07/01/2020 United States 5 02/01/2020 All Sex \n",
"488 07/01/2020 United States 5 02/01/2020 All Sex \n",
".. ... ... ... ... ... \n",
"721 07/01/2020 United States 26 06/27/2020 All Sex \n",
"722 07/01/2020 United States 26 06/27/2020 All Sex \n",
"723 07/01/2020 United States 26 06/27/2020 All Sex \n",
"724 07/01/2020 United States 26 06/27/2020 All Sex \n",
"725 07/01/2020 United States 26 06/27/2020 All Sex \n",
"\n",
" Age Group Total Deaths COVID-19 Deaths \n",
"484 Under 1 year 375 0 \n",
"485 1-4 years 64 0 \n",
"486 5-14 years 110 0 \n",
"487 15-24 years 567 0 \n",
"488 25-34 years 1124 0 \n",
".. ... ... ... \n",
"721 45-54 years 761 18 \n",
"722 55-64 years 1875 32 \n",
"723 65-74 years 3024 45 \n",
"724 75-84 years 4190 53 \n",
"725 85 years and over 5703 78 \n",
"\n",
"[242 rows x 8 columns]"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"whole_us_df"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"total_deaths = whole_us_df.groupby('Age Group').agg({'COVID-19 Deaths': 'sum'})"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
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" <thead>\n",
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" <th></th>\n",
" <th>COVID-19 Deaths</th>\n",
" </tr>\n",
" <tr>\n",
" <th>Age Group</th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1-4 years</th>\n",
" <td>6</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15-24 years</th>\n",
" <td>142</td>\n",
" </tr>\n",
" <tr>\n",
" <th>25-34 years</th>\n",
" <td>770</td>\n",
" </tr>\n",
" <tr>\n",
" <th>35-44 years</th>\n",
" <td>1972</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45-54 years</th>\n",
" <td>5488</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5-14 years</th>\n",
" <td>14</td>\n",
" </tr>\n",
" <tr>\n",
" <th>55-64 years</th>\n",
" <td>13465</td>\n",
" </tr>\n",
" <tr>\n",
" <th>65-74 years</th>\n",
" <td>23333</td>\n",
" </tr>\n",
" <tr>\n",
" <th>75-84 years</th>\n",
" <td>29779</td>\n",
" </tr>\n",
" <tr>\n",
" <th>85 years and over</th>\n",
" <td>37245</td>\n",
" </tr>\n",
" <tr>\n",
" <th>Under 1 year</th>\n",
" <td>9</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
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],
"text/plain": [
" COVID-19 Deaths\n",
"Age Group \n",
"1-4 years 6\n",
"15-24 years 142\n",
"25-34 years 770\n",
"35-44 years 1972\n",
"45-54 years 5488\n",
"5-14 years 14\n",
"55-64 years 13465\n",
"65-74 years 23333\n",
"75-84 years 29779\n",
"85 years and over 37245\n",
"Under 1 year 9"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"total_deaths"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"def convert_item(row):\n",
" if row.name == \"Under 1 year\":\n",
" return [0, 0.9]\n",
" elif row.name == \"85 years and over\":\n",
" return [85, 120]\n",
" else:\n",
" return [float(item) for item in row.name.replace(\" years\", \"\").split(\"-\")]\n",
"\n",
"age_groups = total_deaths.apply(convert_item, axis=1)\n",
"total_deaths['age_groups'] = age_groups\n",
"fixed_index_df = total_deaths.set_index('age_groups')\n",
"sorted_df = fixed_index_df.sort_index()"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
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" <th></th>\n",
" <th>COVID-19 Deaths</th>\n",
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" <td>29779</td>\n",
" </tr>\n",
" <tr>\n",
" <th>[85, 120]</th>\n",
" <td>37245</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" COVID-19 Deaths\n",
"age_groups \n",
"[0, 0.9] 9\n",
"[1.0, 4.0] 6\n",
"[5.0, 14.0] 14\n",
"[15.0, 24.0] 142\n",
"[25.0, 34.0] 770\n",
"[35.0, 44.0] 1972\n",
"[45.0, 54.0] 5488\n",
"[55.0, 64.0] 13465\n",
"[65.0, 74.0] 23333\n",
"[75.0, 84.0] 29779\n",
"[85, 120] 37245"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"sorted_df"
]
},
{
"cell_type": "code",
"execution_count": 15,
"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>% of total deaths</th>\n",
" </tr>\n",
" <tr>\n",
" <th>age_groups</th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
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" <td>0.012</td>\n",
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" <tr>\n",
" <th>[15.0, 24.0]</th>\n",
" <td>0.127</td>\n",
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" <th>[25.0, 34.0]</th>\n",
" <td>0.686</td>\n",
" </tr>\n",
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" <th>[35.0, 44.0]</th>\n",
" <td>1.757</td>\n",
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" <td>4.890</td>\n",
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" <td>11.998</td>\n",
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" <th>[65.0, 74.0]</th>\n",
" <td>20.792</td>\n",
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" <th>[75.0, 84.0]</th>\n",
" <td>26.536</td>\n",
" </tr>\n",
" <tr>\n",
" <th>[85, 120]</th>\n",
" <td>33.188</td>\n",
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"</table>\n",
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"text/plain": [
" % of total deaths\n",
"age_groups \n",
"[0, 0.9] 0.008\n",
"[1.0, 4.0] 0.005\n",
"[5.0, 14.0] 0.012\n",
"[15.0, 24.0] 0.127\n",
"[25.0, 34.0] 0.686\n",
"[35.0, 44.0] 1.757\n",
"[45.0, 54.0] 4.890\n",
"[55.0, 64.0] 11.998\n",
"[65.0, 74.0] 20.792\n",
"[75.0, 84.0] 26.536\n",
"[85, 120] 33.188"
]
},
"execution_count": 15,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"percentages = sorted_df.apply(lambda r: round(100*r/r.sum(),3))\n",
"percentages.rename(columns={\"COVID-19 Deaths\":\"% of total deaths\"})"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
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" <th></th>\n",
" <th>COVID-19 Deaths</th>\n",
" <th>age_groups</th>\n",
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" <tr>\n",
" <th>Age Group</th>\n",
" <th></th>\n",
" <th></th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>1-4 years</th>\n",
" <td>6</td>\n",
" <td>[1.0, 4.0]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>15-24 years</th>\n",
" <td>142</td>\n",
" <td>[15.0, 24.0]</td>\n",
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" <tr>\n",
" <th>25-34 years</th>\n",
" <td>770</td>\n",
" <td>[25.0, 34.0]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>35-44 years</th>\n",
" <td>1972</td>\n",
" <td>[35.0, 44.0]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>45-54 years</th>\n",
" <td>5488</td>\n",
" <td>[45.0, 54.0]</td>\n",
" </tr>\n",
" <tr>\n",
" <th>5-14 years</th>\n",
" <td>14</td>\n",
" <td>[5.0, 14.0]</td>\n",
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" <tr>\n",
" <th>55-64 years</th>\n",
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" <th>85 years and over</th>\n",
" <td>37245</td>\n",
" <td>[85, 120]</td>\n",
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" <th>Under 1 year</th>\n",
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" <td>[0, 0.9]</td>\n",
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"</table>\n",
"</div>"
],
"text/plain": [
" COVID-19 Deaths age_groups\n",
"Age Group \n",
"1-4 years 6 [1.0, 4.0]\n",
"15-24 years 142 [15.0, 24.0]\n",
"25-34 years 770 [25.0, 34.0]\n",
"35-44 years 1972 [35.0, 44.0]\n",
"45-54 years 5488 [45.0, 54.0]\n",
"5-14 years 14 [5.0, 14.0]\n",
"55-64 years 13465 [55.0, 64.0]\n",
"65-74 years 23333 [65.0, 74.0]\n",
"75-84 years 29779 [75.0, 84.0]\n",
"85 years and over 37245 [85, 120]\n",
"Under 1 year 9 [0, 0.9]"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"total_deaths"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
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]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"fig = px.pie(total_deaths, values=\"COVID-19 Deaths\", names=\"age_groups\")\n",
"fig.show(renderer=\"svg\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.7.7"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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