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{ | ||
"cells": [ | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 1, | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"import pandas as pd\n", | ||
"import numpy as np\n", | ||
"from datetime import date,time,timedelta\n", | ||
"\n", | ||
"path_cases = 'https://moh-malaysia-covid19.s3.ap-southeast-1.amazonaws.com/linelist_cases.parquet'\n", | ||
"path_param_geo = 'https://raw.githubusercontent.com/MoH-Malaysia/covid19-public/main/epidemic/linelist/param_geo.csv'\n" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 2, | ||
"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>state</th>\n", | ||
" <th>district</th>\n", | ||
" </tr>\n", | ||
" </thead>\n", | ||
" <tbody>\n", | ||
" <tr>\n", | ||
" <th>0</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Johor Bahru</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>1</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Johor Bahru</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>2</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Johor Bahru</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>3</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Johor Bahru</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>4</th>\n", | ||
" <td>2020-01-29</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Johor Bahru</td>\n", | ||
" </tr>\n", | ||
" </tbody>\n", | ||
"</table>\n", | ||
"</div>" | ||
], | ||
"text/plain": [ | ||
" date state district\n", | ||
"0 2020-01-25 Johor Johor Bahru\n", | ||
"1 2020-01-25 Johor Johor Bahru\n", | ||
"2 2020-01-25 Johor Johor Bahru\n", | ||
"3 2020-01-25 Johor Johor Bahru\n", | ||
"4 2020-01-29 Johor Johor Bahru" | ||
] | ||
}, | ||
"execution_count": 2, | ||
"metadata": {}, | ||
"output_type": "execute_result" | ||
} | ||
], | ||
"source": [ | ||
"geo = pd.read_csv(path_param_geo)\n", | ||
"idxd_district = dict(zip(geo.idxd, geo.district))\n", | ||
"idxs_state = dict(zip(geo.idxs, geo.state))\n", | ||
"district_state = dict(zip(geo.district, geo.state))\n", | ||
"\n", | ||
"df = pd.read_parquet(path_cases, columns=['date', 'state', 'district'])\n", | ||
"df['state'] = df.state.map(idxs_state)\n", | ||
"df['district'] = df.district.map(idxd_district)\n", | ||
"df.head()" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 3, | ||
"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>state</th>\n", | ||
" <th>district</th>\n", | ||
" <th>cases</th>\n", | ||
" </tr>\n", | ||
" </thead>\n", | ||
" <tbody>\n", | ||
" <tr>\n", | ||
" <th>0</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Batu Pahat</td>\n", | ||
" <td>0</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>1</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Johor Bahru</td>\n", | ||
" <td>4</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>2</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Kluang</td>\n", | ||
" <td>0</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>3</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Kota Tinggi</td>\n", | ||
" <td>0</td>\n", | ||
" </tr>\n", | ||
" <tr>\n", | ||
" <th>4</th>\n", | ||
" <td>2020-01-25</td>\n", | ||
" <td>Johor</td>\n", | ||
" <td>Kulai</td>\n", | ||
" <td>0</td>\n", | ||
" </tr>\n", | ||
" </tbody>\n", | ||
"</table>\n", | ||
"</div>" | ||
], | ||
"text/plain": [ | ||
" date state district cases\n", | ||
"0 2020-01-25 Johor Batu Pahat 0\n", | ||
"1 2020-01-25 Johor Johor Bahru 4\n", | ||
"2 2020-01-25 Johor Kluang 0\n", | ||
"3 2020-01-25 Johor Kota Tinggi 0\n", | ||
"4 2020-01-25 Johor Kulai 0" | ||
] | ||
}, | ||
"execution_count": 3, | ||
"metadata": {}, | ||
"output_type": "execute_result" | ||
} | ||
], | ||
"source": [ | ||
"df = df[~df.district.isnull()].copy()\n", | ||
"df.date = pd.to_datetime(df.date)\n", | ||
"df['cases'] = 1\n", | ||
"\n", | ||
"df = df.groupby(['date','district'])\\\n", | ||
" .sum()\\\n", | ||
" .unstack(fill_value=0)\\\n", | ||
" .asfreq('D', fill_value=0)\\\n", | ||
" .stack()\\\n", | ||
" .sort_index(level=1)\\\n", | ||
" .reset_index()\n", | ||
"df.date = df.date.dt.date\n", | ||
"df['state'] = df.district.map(district_state)\n", | ||
"df = df[['date','state','district','cases']]\n", | ||
"df = df.sort_values(by=['date','state','district']).reset_index(drop=True)\n", | ||
"df.head()" | ||
] | ||
} | ||
], | ||
"metadata": { | ||
"kernelspec": { | ||
"display_name": "Python 3.9.6 ('pipenv')", | ||
"language": "python", | ||
"name": "python3" | ||
}, | ||
"language_info": { | ||
"codemirror_mode": { | ||
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"nbformat": 4, | ||
"nbformat_minor": 2 | ||
} |
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