notebooks/data_summary.ipynb

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   "source": [
    "# Quick analysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
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   "source": [
    "## Import libraries\n",
    "\n",
    "%load_ext autoreload\n",
    "%autoreload 2\n",
    "\n",
    "import os\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "from datetime import date, datetime\n",
    "from IPython.display import display, Markdown\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "2022-03-22\n"
     ]
    }
   ],
   "source": [
    "# import data\n",
    "\n",
    "#df = pd.read_csv(\"../output/input.csv\")\n",
    "df = pd.read_feather(\"../output/input.feather\")\n",
    "#df[\"hospital_admission_date\"] = df[\"hospital_admission_date\"].fillna(\"1900-01-01\")\n",
    "\n",
    "maxdate = df[\"hospital_admission_date\"].max()\n",
    "print(maxdate)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "### MABs"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
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     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "        vertical-align: middle;\n",
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       "\n",
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       "    }\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>count</th>\n",
       "      <th>percent</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>outpatient_covid_therapeutic_date</th>\n",
       "      <td>250</td>\n",
       "      <td>100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sus_treatment_date</th>\n",
       "      <td>27</td>\n",
       "      <td>10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_admission_date</th>\n",
       "      <td>250</td>\n",
       "      <td>100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_admission_x892_date</th>\n",
       "      <td>13</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_admission_x292_date</th>\n",
       "      <td>9</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_attendance_date</th>\n",
       "      <td>13</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                   count  percent\n",
       "outpatient_covid_therapeutic_date    250      100\n",
       "sus_treatment_date                    27       10\n",
       "hospital_admission_date              250      100\n",
       "hospital_admission_x892_date          13        5\n",
       "hospital_admission_x292_date           9        3\n",
       "hospital_attendance_date              13        5"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/markdown": [
       "### Antivirals"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>count</th>\n",
       "      <th>percent</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>outpatient_covid_therapeutic_date</th>\n",
       "      <td>388</td>\n",
       "      <td>100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sus_treatment_date</th>\n",
       "      <td>39</td>\n",
       "      <td>10</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_admission_date</th>\n",
       "      <td>388</td>\n",
       "      <td>100</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_admission_x892_date</th>\n",
       "      <td>17</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_admission_x292_date</th>\n",
       "      <td>23</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>hospital_attendance_date</th>\n",
       "      <td>20</td>\n",
       "      <td>5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                   count  percent\n",
       "outpatient_covid_therapeutic_date    388      100\n",
       "sus_treatment_date                    39       10\n",
       "hospital_admission_date              388      100\n",
       "hospital_admission_x892_date          17        4\n",
       "hospital_admission_x292_date          23        5\n",
       "hospital_attendance_date              20        5"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "df1 = df.loc[df[\"outpatient_covid_therapeutic_date\"] <= maxdate]\n",
    "treatments = {\"MABs\":['sotrovimab', 'casirivimab and imdevimab'],\n",
    "       \"Antivirals\":['paxlovid', 'remdesivir', 'molnupiravir']}\n",
    "\n",
    "for t in treatments:\n",
    "    df_t = df1.loc[df1[\"outpatient_covid_therapeutic_name\"].isin(treatments[t])]\n",
    "    summary1 = pd.DataFrame(df_t[[\"outpatient_covid_therapeutic_date\", \"sus_treatment_date\",\n",
    "                            \"hospital_admission_date\",\"hospital_admission_x892_date\",\"hospital_admission_x292_date\",\n",
    "                            \"hospital_attendance_date\"]].count()).rename(columns={0:\"count\"})\n",
    "    summary1[\"percent\"] = (100*(summary1[\"count\"]/summary1[\"count\"][\"outpatient_covid_therapeutic_date\"])).round(2).astype(int)\n",
    "    display(Markdown(f\"### {t}\"), summary1)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Breakdown by region and age group"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "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>outpatient_covid_therapeutic_date</th>\n",
       "      <th>sus_treatment_date</th>\n",
       "      <th>percent</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>region_covid_therapeutics</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>East</th>\n",
       "      <td>17</td>\n",
       "      <td>2</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>East Midlands</th>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>London</th>\n",
       "      <td>52</td>\n",
       "      <td>7</td>\n",
       "      <td>13</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>North East</th>\n",
       "      <td>26</td>\n",
       "      <td>2</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>North West</th>\n",
       "      <td>27</td>\n",
       "      <td>3</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>South East</th>\n",
       "      <td>29</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>South West</th>\n",
       "      <td>41</td>\n",
       "      <td>7</td>\n",
       "      <td>17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>West Midlands</th>\n",
       "      <td>18</td>\n",
       "      <td>2</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Yorkshire and The Humber</th>\n",
       "      <td>13</td>\n",
       "      <td>1</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                           outpatient_covid_therapeutic_date  \\\n",
       "region_covid_therapeutics                                      \n",
       "East                                                      17   \n",
       "East Midlands                                             27   \n",
       "London                                                    52   \n",
       "North East                                                26   \n",
       "North West                                                27   \n",
       "South East                                                29   \n",
       "South West                                                41   \n",
       "West Midlands                                             18   \n",
       "Yorkshire and The Humber                                  13   \n",
       "\n",
       "                           sus_treatment_date  percent  \n",
       "region_covid_therapeutics                               \n",
       "East                                        2       11  \n",
       "East Midlands                               1        3  \n",
       "London                                      7       13  \n",
       "North East                                  2        7  \n",
       "North West                                  3       11  \n",
       "South East                                  2        6  \n",
       "South West                                  7       17  \n",
       "West Midlands                               2       11  \n",
       "Yorkshire and The Humber                    1        7  "
      ]
     },
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>outpatient_covid_therapeutic_date</th>\n",
       "      <th>sus_treatment_date</th>\n",
       "      <th>percent</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>age_group</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>12-24</th>\n",
       "      <td>27</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25-34</th>\n",
       "      <td>22</td>\n",
       "      <td>4</td>\n",
       "      <td>18</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>35-44</th>\n",
       "      <td>44</td>\n",
       "      <td>5</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>45-54</th>\n",
       "      <td>56</td>\n",
       "      <td>9</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>55-64</th>\n",
       "      <td>25</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>65-74</th>\n",
       "      <td>23</td>\n",
       "      <td>2</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75+</th>\n",
       "      <td>22</td>\n",
       "      <td>2</td>\n",
       "      <td>9</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>missing</th>\n",
       "      <td>31</td>\n",
       "      <td>2</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
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      ],
      "text/plain": [
       "           outpatient_covid_therapeutic_date  sus_treatment_date  percent\n",
       "age_group                                                                \n",
       "12-24                                     27                   1        3\n",
       "25-34                                     22                   4       18\n",
       "35-44                                     44                   5       11\n",
       "45-54                                     56                   9       16\n",
       "55-64                                     25                   2        8\n",
       "65-74                                     23                   2        8\n",
       "75+                                       22                   2        9\n",
       "missing                                   31                   2        6"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "# mabs only\n",
    "df_m = df1.loc[df1[\"outpatient_covid_therapeutic_name\"].isin(treatments[\"MABs\"])]\n",
    "\n",
    "for col in [\"region_covid_therapeutics\",\"age_group\"]:\n",
    "    summary2 = pd.DataFrame(df_m.groupby(col)\\\n",
    "               [[\"outpatient_covid_therapeutic_date\",\"sus_treatment_date\"]].count()).rename(columns={0:\"count\"})\n",
    "    summary2[\"percent\"] = (100*summary2[\"sus_treatment_date\"]/summary2[\"outpatient_covid_therapeutic_date\"]).round(2).astype(int)\n",
    "    display(summary2)"
   ]
  }
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