tidy up notebooks

MoH-Malaysia · Aug 11, 2022 · 2e5bf0e · 2e5bf0e
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diff --git a/notebooks/cases_by_district.ipynb b/notebooks/cases_by_district.ipynb
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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()"
+ ]
+ }
+ ],
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+ "kernelspec": {
+ "display_name": "Python 3.9.6 ('pipenv')",
+ "language": "python",
+ "name": "python3"
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