From 1705e7314cf2c29a4bc0930171722899f57e8865 Mon Sep 17 00:00:00 2001
From: CITF <87315214+MoH-Malaysia@users.noreply.github.com>
Date: Mon, 21 Mar 2022 21:05:44 +0800
Subject: [PATCH] Create deaths_capita_vaxstatus_ts.ipynb

---
 notebooks/deaths_capita_vaxstatus_ts.ipynb | 470 +++++++++++++++++++++
 1 file changed, 470 insertions(+)
 create mode 100644 notebooks/deaths_capita_vaxstatus_ts.ipynb

diff --git a/notebooks/deaths_capita_vaxstatus_ts.ipynb b/notebooks/deaths_capita_vaxstatus_ts.ipynb
new file mode 100644
index 000000000..e2d3b13b3
--- /dev/null
+++ b/notebooks/deaths_capita_vaxstatus_ts.ipynb
@@ -0,0 +1,470 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "22b06768",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "from datetime import date, timedelta\n",
+    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.dates as mdates\n",
+    "\n",
+    "linelist_deaths = 'https://raw.githubusercontent.com/MoH-Malaysia/covid19-public/main/epidemic/linelist/linelist_deaths.csv'\n",
+    "vax_agg = 'https://raw.githubusercontent.com/MoH-Malaysia/covid19-public/main/vaccination/vax_malaysia.csv'\n",
+    "\n",
+    "date_min = date(2021,5,24) # Phase 2 vax started 19 Apr; 2nd dose on 10 May; fully vax on 24 May\n",
+    "date_max = date.today() - timedelta(8) # most recent 7 days incomplete\n",
+    "data_range = 'data from ' + date_min.strftime('%d-%b') + ' to ' + date_max.strftime('%d-%b')\n",
+    "total_adults = 23966637 # same as other notebooks"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "35140c24",
+   "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>status</th>\n",
+       "      <th>deaths</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>1152</th>\n",
+       "      <td>2022-03-08</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>14</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1153</th>\n",
+       "      <td>2022-03-08</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>37</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1155</th>\n",
+       "      <td>2022-03-08</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>22</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1156</th>\n",
+       "      <td>2022-03-09</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>20</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1157</th>\n",
+       "      <td>2022-03-09</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>33</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1159</th>\n",
+       "      <td>2022-03-09</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>33</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1160</th>\n",
+       "      <td>2022-03-10</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>21</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1161</th>\n",
+       "      <td>2022-03-10</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>39</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1163</th>\n",
+       "      <td>2022-03-10</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>18</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1164</th>\n",
+       "      <td>2022-03-11</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>13</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1165</th>\n",
+       "      <td>2022-03-11</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>39</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1167</th>\n",
+       "      <td>2022-03-11</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>22</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1168</th>\n",
+       "      <td>2022-03-12</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>23</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1169</th>\n",
+       "      <td>2022-03-12</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>52</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1171</th>\n",
+       "      <td>2022-03-12</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>32</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1172</th>\n",
+       "      <td>2022-03-13</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>25</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1173</th>\n",
+       "      <td>2022-03-13</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>35</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1175</th>\n",
+       "      <td>2022-03-13</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>25</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "            date    status  deaths\n",
+       "1152  2022-03-08   boosted      14\n",
+       "1153  2022-03-08  fullyvax      37\n",
+       "1155  2022-03-08     unvax      22\n",
+       "1156  2022-03-09   boosted      20\n",
+       "1157  2022-03-09  fullyvax      33\n",
+       "1159  2022-03-09     unvax      33\n",
+       "1160  2022-03-10   boosted      21\n",
+       "1161  2022-03-10  fullyvax      39\n",
+       "1163  2022-03-10     unvax      18\n",
+       "1164  2022-03-11   boosted      13\n",
+       "1165  2022-03-11  fullyvax      39\n",
+       "1167  2022-03-11     unvax      22\n",
+       "1168  2022-03-12   boosted      23\n",
+       "1169  2022-03-12  fullyvax      52\n",
+       "1171  2022-03-12     unvax      32\n",
+       "1172  2022-03-13   boosted      25\n",
+       "1173  2022-03-13  fullyvax      35\n",
+       "1175  2022-03-13     unvax      25"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "def vaxStatus(date_pos, date1, date2, date3):\n",
+    "    if (date_pos - date3).days > 6: return 'boosted'\n",
+    "    elif (date_pos - date2).days > 13: return 'fullyvax'\n",
+    "    elif (date_pos - date1).days >= 0: return 'partialvax'\n",
+    "    else: return 'unvax'\n",
+    "    \n",
+    "\n",
+    "# Pull latest deaths linelist and wrangle\n",
+    "cols_date = ['date', 'date_positive', 'date_dose1', 'date_dose2', 'date_dose3']\n",
+    "df = pd.read_csv(linelist_deaths,\n",
+    "                 usecols=cols_date + ['brand1','age'])\n",
+    "for c in cols_date: df[c] = pd.to_datetime(df[c],errors='coerce').dt.date\n",
+    "df = df[(df.date >= date_min) & (df.date <= date_max)]\n",
+    "df = df[df.age > 17] # adults only\n",
+    "df.drop(['age'],axis=1,inplace=True)\n",
+    "\n",
+    "# Ensure no null vax dates (future date as placeholder), shift 14 days for Cansino, then encode vax status\n",
+    "for c in ['date_dose1', 'date_dose2', 'date_dose3']: df[c] = df[c].fillna(date.today() + timedelta(1))\n",
+    "df.loc[df.brand1.isin(['Cansino']), 'date_dose2'] = df.date_dose1 + timedelta(14)\n",
+    "df['status'] = df.apply(lambda x: vaxStatus(x['date_positive'], x['date_dose1'], x['date_dose2'], x['date_dose3']), axis=1)\n",
+    "df = df.replace(date.today() + timedelta(1), np.nan)  # Remove placeholder dates\n",
+    "df['deaths'] = 1\n",
+    "\n",
+    "df.date = pd.to_datetime(df.date)\n",
+    "df = df.groupby(['date', 'status']).sum() \\\n",
+    "                .unstack(fill_value=0) \\\n",
+    "                .asfreq('D',fill_value=0) \\\n",
+    "                .stack() \\\n",
+    "                .reset_index() # Typically, unstack/stack suffices, but this is robust to having dates with no deaths\n",
+    "df.date = df.date.dt.date\n",
+    "df = df[~df.status.isin(['partialvax'])]\n",
+    "df[-18:].head(18)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "00d778d2",
+   "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>status</th>\n",
+       "      <th>population</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>1547</th>\n",
+       "      <td>2022-03-08</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>14759732</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1157</th>\n",
+       "      <td>2022-03-08</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>8719041</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>377</th>\n",
+       "      <td>2022-03-08</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>758016</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1548</th>\n",
+       "      <td>2022-03-09</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>14830764</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1158</th>\n",
+       "      <td>2022-03-09</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>8622531</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>378</th>\n",
+       "      <td>2022-03-09</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>757120</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1549</th>\n",
+       "      <td>2022-03-10</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>14903527</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1159</th>\n",
+       "      <td>2022-03-10</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>8532850</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>379</th>\n",
+       "      <td>2022-03-10</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>756138</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1550</th>\n",
+       "      <td>2022-03-11</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>14961911</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1160</th>\n",
+       "      <td>2022-03-11</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>8445111</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>380</th>\n",
+       "      <td>2022-03-11</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>755183</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1551</th>\n",
+       "      <td>2022-03-12</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>15000150</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1161</th>\n",
+       "      <td>2022-03-12</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>8381290</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>381</th>\n",
+       "      <td>2022-03-12</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>754344</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1552</th>\n",
+       "      <td>2022-03-13</td>\n",
+       "      <td>boosted</td>\n",
+       "      <td>15032666</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1162</th>\n",
+       "      <td>2022-03-13</td>\n",
+       "      <td>fullyvax</td>\n",
+       "      <td>8322054</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>382</th>\n",
+       "      <td>2022-03-13</td>\n",
+       "      <td>unvax</td>\n",
+       "      <td>753674</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "            date    status  population\n",
+       "1547  2022-03-08   boosted    14759732\n",
+       "1157  2022-03-08  fullyvax     8719041\n",
+       "377   2022-03-08     unvax      758016\n",
+       "1548  2022-03-09   boosted    14830764\n",
+       "1158  2022-03-09  fullyvax     8622531\n",
+       "378   2022-03-09     unvax      757120\n",
+       "1549  2022-03-10   boosted    14903527\n",
+       "1159  2022-03-10  fullyvax     8532850\n",
+       "379   2022-03-10     unvax      756138\n",
+       "1550  2022-03-11   boosted    14961911\n",
+       "1160  2022-03-11  fullyvax     8445111\n",
+       "380   2022-03-11     unvax      755183\n",
+       "1551  2022-03-12   boosted    15000150\n",
+       "1161  2022-03-12  fullyvax     8381290\n",
+       "381   2022-03-12     unvax      754344\n",
+       "1552  2022-03-13   boosted    15032666\n",
+       "1162  2022-03-13  fullyvax     8322054\n",
+       "382   2022-03-13     unvax      753674"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "shifts = {'cumul_partial_adult': 1, 'cumul_full_adult': 14, 'cumul_booster':7}\n",
+    "vf = pd.read_csv(vax_agg)\n",
+    "vf.date = pd.to_datetime(vf.date).dt.date\n",
+    "vf['cumul_partial_adult'] = vf.cumul_partial - vf.cumul_partial_adol - vf.cumul_partial_child\n",
+    "vf['unvax_adult'] = total_adults - vf.cumul_partial_adult\n",
+    "vf['cumul_full_adult'] = vf.cumul_full - vf.cumul_full_adol - vf.cumul_full_child - vf.cumul_booster\n",
+    "vf['cumul_partial_adult'] = vf['cumul_partial_adult'] - vf['cumul_full_adult'] - vf.cumul_booster\n",
+    "\n",
+    "for c in ['cumul_partial_adult', 'cumul_full_adult','cumul_booster']: vf[c] = vf[c].shift(shifts[c]).fillna(0).astype(int)\n",
+    "vf = vf[['date','unvax_adult','cumul_partial_adult','cumul_full_adult','cumul_booster']]\n",
+    "col_status = ['unvax','partialvax','fullyvax','boosted']\n",
+    "vf.columns = ['date'] + col_status\n",
+    "vf = pd.melt(vf, id_vars=['date'], value_vars=col_status)\n",
+    "vf.columns = ['date','status','population']\n",
+    "vf = vf[(vf.date >= date_min) & (vf.date <= date_max)]\n",
+    "vf = vf[~vf.status.isin(['partialvax'])].sort_values(by=['date','status']).reset_index(drop=True)\n",
+    "vf[-18:].head(18)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "34bd49f1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Merge frames and compute incidence, then get 7d rolling average\n",
+    "df = pd.merge(df,vf, on=['date','status'], how='left')\n",
+    "df['capita'] = df.deaths/df.population * 1e5\n",
+    "df = df.pivot(index='date', columns='status', values=['capita']).fillna(0).reset_index()\n",
+    "df.columns = ['date','Boosted','Fully Vaccinated','Unvaccinated']\n",
+    "df = df[['date','Unvaccinated','Fully Vaccinated','Boosted']].set_index('date')\n",
+    "df = df.rolling(7).mean().reset_index()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "54685078",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.9.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}