data_exploration.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 201,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "The autoreload extension is already loaded. To reload it, use:\n",
      "  %reload_ext autoreload\n"
     ]
    }
   ],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 202,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd \n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "import seaborn as sns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 203,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_excel('data/dataset.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 204,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<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>Patient ID</th>\n",
       "      <th>Patient age quantile</th>\n",
       "      <th>SARS-Cov-2 exam result</th>\n",
       "      <th>Patient addmited to regular ward (1=yes, 0=no)</th>\n",
       "      <th>Patient addmited to semi-intensive unit (1=yes, 0=no)</th>\n",
       "      <th>Patient addmited to intensive care unit (1=yes, 0=no)</th>\n",
       "      <th>Hematocrit</th>\n",
       "      <th>Hemoglobin</th>\n",
       "      <th>Platelets</th>\n",
       "      <th>Mean platelet volume</th>\n",
       "      <th>Red blood Cells</th>\n",
       "      <th>Lymphocytes</th>\n",
       "      <th>Mean corpuscular hemoglobin concentration (MCHC)</th>\n",
       "      <th>Leukocytes</th>\n",
       "      <th>Basophils</th>\n",
       "      <th>Mean corpuscular hemoglobin (MCH)</th>\n",
       "      <th>Eosinophils</th>\n",
       "      <th>Mean corpuscular volume (MCV)</th>\n",
       "      <th>Monocytes</th>\n",
       "      <th>Red blood cell distribution width (RDW)</th>\n",
       "      <th>Serum Glucose</th>\n",
       "      <th>Respiratory Syncytial Virus</th>\n",
       "      <th>Influenza A</th>\n",
       "      <th>Influenza B</th>\n",
       "      <th>Parainfluenza 1</th>\n",
       "      <th>CoronavirusNL63</th>\n",
       "      <th>Rhinovirus/Enterovirus</th>\n",
       "      <th>Mycoplasma pneumoniae</th>\n",
       "      <th>Coronavirus HKU1</th>\n",
       "      <th>Parainfluenza 3</th>\n",
       "      <th>Chlamydophila pneumoniae</th>\n",
       "      <th>Adenovirus</th>\n",
       "      <th>Parainfluenza 4</th>\n",
       "      <th>Coronavirus229E</th>\n",
       "      <th>CoronavirusOC43</th>\n",
       "      <th>Inf A H1N1 2009</th>\n",
       "      <th>Bordetella pertussis</th>\n",
       "      <th>Metapneumovirus</th>\n",
       "      <th>Parainfluenza 2</th>\n",
       "      <th>Neutrophils</th>\n",
       "      <th>Urea</th>\n",
       "      <th>Proteina C reativa mg/dL</th>\n",
       "      <th>Creatinine</th>\n",
       "      <th>Potassium</th>\n",
       "      <th>Sodium</th>\n",
       "      <th>Influenza B, rapid test</th>\n",
       "      <th>Influenza A, rapid test</th>\n",
       "      <th>Alanine transaminase</th>\n",
       "      <th>Aspartate transaminase</th>\n",
       "      <th>Gamma-glutamyltransferase</th>\n",
       "      <th>Total Bilirubin</th>\n",
       "      <th>Direct Bilirubin</th>\n",
       "      <th>Indirect Bilirubin</th>\n",
       "      <th>Alkaline phosphatase</th>\n",
       "      <th>Ionized calcium</th>\n",
       "      <th>Strepto A</th>\n",
       "      <th>Magnesium</th>\n",
       "      <th>pCO2 (venous blood gas analysis)</th>\n",
       "      <th>Hb saturation (venous blood gas analysis)</th>\n",
       "      <th>Base excess (venous blood gas analysis)</th>\n",
       "      <th>pO2 (venous blood gas analysis)</th>\n",
       "      <th>Fio2 (venous blood gas analysis)</th>\n",
       "      <th>Total CO2 (venous blood gas analysis)</th>\n",
       "      <th>pH (venous blood gas analysis)</th>\n",
       "      <th>HCO3 (venous blood gas analysis)</th>\n",
       "      <th>Rods #</th>\n",
       "      <th>Segmented</th>\n",
       "      <th>Promyelocytes</th>\n",
       "      <th>Metamyelocytes</th>\n",
       "      <th>Myelocytes</th>\n",
       "      <th>Myeloblasts</th>\n",
       "      <th>Urine - Esterase</th>\n",
       "      <th>Urine - Aspect</th>\n",
       "      <th>Urine - pH</th>\n",
       "      <th>Urine - Hemoglobin</th>\n",
       "      <th>Urine - Bile pigments</th>\n",
       "      <th>Urine - Ketone Bodies</th>\n",
       "      <th>Urine - Nitrite</th>\n",
       "      <th>Urine - Density</th>\n",
       "      <th>Urine - Urobilinogen</th>\n",
       "      <th>Urine - Protein</th>\n",
       "      <th>Urine - Sugar</th>\n",
       "      <th>Urine - Leukocytes</th>\n",
       "      <th>Urine - Crystals</th>\n",
       "      <th>Urine - Red blood cells</th>\n",
       "      <th>Urine - Hyaline cylinders</th>\n",
       "      <th>Urine - Granular cylinders</th>\n",
       "      <th>Urine - Yeasts</th>\n",
       "      <th>Urine - Color</th>\n",
       "      <th>Partial thromboplastin time (PTT)</th>\n",
       "      <th>Relationship (Patient/Normal)</th>\n",
       "      <th>International normalized ratio (INR)</th>\n",
       "      <th>Lactic Dehydrogenase</th>\n",
       "      <th>Prothrombin time (PT), Activity</th>\n",
       "      <th>Vitamin B12</th>\n",
       "      <th>Creatine phosphokinase (CPK)</th>\n",
       "      <th>Ferritin</th>\n",
       "      <th>Arterial Lactic Acid</th>\n",
       "      <th>Lipase dosage</th>\n",
       "      <th>D-Dimer</th>\n",
       "      <th>Albumin</th>\n",
       "      <th>Hb saturation (arterial blood gases)</th>\n",
       "      <th>pCO2 (arterial blood gas analysis)</th>\n",
       "      <th>Base excess (arterial blood gas analysis)</th>\n",
       "      <th>pH (arterial blood gas analysis)</th>\n",
       "      <th>Total CO2 (arterial blood gas analysis)</th>\n",
       "      <th>HCO3 (arterial blood gas analysis)</th>\n",
       "      <th>pO2 (arterial blood gas analysis)</th>\n",
       "      <th>Arteiral Fio2</th>\n",
       "      <th>Phosphor</th>\n",
       "      <th>ctO2 (arterial blood gas analysis)</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
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       "    <tr>\n",
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       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>d9e41465789c2b5</td>\n",
       "      <td>15</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>75f16746216c4d1</td>\n",
       "      <td>9</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>2a2245e360808d7</td>\n",
       "      <td>13</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>509197ec73f1400</td>\n",
       "      <td>16</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>8bb9d64f0215244</td>\n",
       "      <td>1</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>-1.571682</td>\n",
       "      <td>-0.774212</td>\n",
       "      <td>1.429667</td>\n",
       "      <td>-1.672222</td>\n",
       "      <td>-0.850035</td>\n",
       "      <td>-0.005738</td>\n",
       "      <td>3.331071</td>\n",
       "      <td>0.36455</td>\n",
       "      <td>-0.223767</td>\n",
       "      <td>0.178175</td>\n",
       "      <td>1.018625</td>\n",
       "      <td>-1.336024</td>\n",
       "      <td>0.068652</td>\n",
       "      <td>-0.978899</td>\n",
       "      <td>-0.413208</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>-0.127395</td>\n",
       "      <td>-0.067309</td>\n",
       "      <td>-0.286986</td>\n",
       "      <td>-1.838623</td>\n",
       "      <td>0.930020</td>\n",
       "      <td>0.503132</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.586821</td>\n",
       "      <td>-0.1622</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.724353</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.075153</td>\n",
       "      <td>0.615594</td>\n",
       "      <td>-0.554737</td>\n",
       "      <td>-0.283748</td>\n",
       "      <td>-0.562902</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.104088</td>\n",
       "      <td>-0.855513</td>\n",
       "      <td>0.036345</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.089481</td>\n",
       "      <td>0.296546</td>\n",
       "      <td>0.907723</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.267856</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.730393</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>5f1ed301375586c</td>\n",
       "      <td>17</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "        Patient ID  Patient age quantile SARS-Cov-2 exam result  \\\n",
       "0  44477f75e8169d2                    13               negative   \n",
       "1  126e9dd13932f68                    17               negative   \n",
       "2  a46b4402a0e5696                     8               negative   \n",
       "3  f7d619a94f97c45                     5               negative   \n",
       "4  d9e41465789c2b5                    15               negative   \n",
       "5  75f16746216c4d1                     9               negative   \n",
       "6  2a2245e360808d7                    13               negative   \n",
       "7  509197ec73f1400                    16               negative   \n",
       "8  8bb9d64f0215244                     1               negative   \n",
       "9  5f1ed301375586c                    17               negative   \n",
       "\n",
       "   Patient addmited to regular ward (1=yes, 0=no)  \\\n",
       "0                                               0   \n",
       "1                                               0   \n",
       "2                                               0   \n",
       "3                                               0   \n",
       "4                                               0   \n",
       "5                                               0   \n",
       "6                                               0   \n",
       "7                                               0   \n",
       "8                                               0   \n",
       "9                                               0   \n",
       "\n",
       "   Patient addmited to semi-intensive unit (1=yes, 0=no)  \\\n",
       "0                                                  0       \n",
       "1                                                  0       \n",
       "2                                                  0       \n",
       "3                                                  0       \n",
       "4                                                  0       \n",
       "5                                                  0       \n",
       "6                                                  0       \n",
       "7                                                  0       \n",
       "8                                                  1       \n",
       "9                                                  0       \n",
       "\n",
       "   Patient addmited to intensive care unit (1=yes, 0=no)  Hematocrit  \\\n",
       "0                                                  0             NaN   \n",
       "1                                                  0        0.236515   \n",
       "2                                                  0             NaN   \n",
       "3                                                  0             NaN   \n",
       "4                                                  0             NaN   \n",
       "5                                                  0             NaN   \n",
       "6                                                  0             NaN   \n",
       "7                                                  0             NaN   \n",
       "8                                                  0       -1.571682   \n",
       "9                                                  0             NaN   \n",
       "\n",
       "   Hemoglobin  Platelets  Mean platelet volume   Red blood Cells  Lymphocytes  \\\n",
       "0         NaN        NaN                    NaN              NaN          NaN   \n",
       "1   -0.022340  -0.517413               0.010677         0.102004     0.318366   \n",
       "2         NaN        NaN                    NaN              NaN          NaN   \n",
       "3         NaN        NaN                    NaN              NaN          NaN   \n",
       "4         NaN        NaN                    NaN              NaN          NaN   \n",
       "5         NaN        NaN                    NaN              NaN          NaN   \n",
       "6         NaN        NaN                    NaN              NaN          NaN   \n",
       "7         NaN        NaN                    NaN              NaN          NaN   \n",
       "8   -0.774212   1.429667              -1.672222        -0.850035    -0.005738   \n",
       "9         NaN        NaN                    NaN              NaN          NaN   \n",
       "\n",
       "   Mean corpuscular hemoglobin concentration (MCHC)  Leukocytes  Basophils  \\\n",
       "0                                               NaN         NaN        NaN   \n",
       "1                                         -0.950790    -0.09461  -0.223767   \n",
       "2                                               NaN         NaN        NaN   \n",
       "3                                               NaN         NaN        NaN   \n",
       "4                                               NaN         NaN        NaN   \n",
       "5                                               NaN         NaN        NaN   \n",
       "6                                               NaN         NaN        NaN   \n",
       "7                                               NaN         NaN        NaN   \n",
       "8                                          3.331071     0.36455  -0.223767   \n",
       "9                                               NaN         NaN        NaN   \n",
       "\n",
       "   Mean corpuscular hemoglobin (MCH)  Eosinophils  \\\n",
       "0                                NaN          NaN   \n",
       "1                          -0.292269     1.482158   \n",
       "2                                NaN          NaN   \n",
       "3                                NaN          NaN   \n",
       "4                                NaN          NaN   \n",
       "5                                NaN          NaN   \n",
       "6                                NaN          NaN   \n",
       "7                                NaN          NaN   \n",
       "8                           0.178175     1.018625   \n",
       "9                                NaN          NaN   \n",
       "\n",
       "   Mean corpuscular volume (MCV)  Monocytes  \\\n",
       "0                            NaN        NaN   \n",
       "1                       0.166192   0.357547   \n",
       "2                            NaN        NaN   \n",
       "3                            NaN        NaN   \n",
       "4                            NaN        NaN   \n",
       "5                            NaN        NaN   \n",
       "6                            NaN        NaN   \n",
       "7                            NaN        NaN   \n",
       "8                      -1.336024   0.068652   \n",
       "9                            NaN        NaN   \n",
       "\n",
       "   Red blood cell distribution width (RDW)  Serum Glucose  \\\n",
       "0                                      NaN            NaN   \n",
       "1                                -0.625073      -0.140648   \n",
       "2                                      NaN            NaN   \n",
       "3                                      NaN            NaN   \n",
       "4                                      NaN            NaN   \n",
       "5                                      NaN            NaN   \n",
       "6                                      NaN            NaN   \n",
       "7                                      NaN            NaN   \n",
       "8                                -0.978899      -0.413208   \n",
       "9                                      NaN            NaN   \n",
       "\n",
       "  Respiratory Syncytial Virus   Influenza A   Influenza B Parainfluenza 1  \\\n",
       "0                         NaN           NaN           NaN             NaN   \n",
       "1                not_detected  not_detected  not_detected    not_detected   \n",
       "2                         NaN           NaN           NaN             NaN   \n",
       "3                         NaN           NaN           NaN             NaN   \n",
       "4                not_detected  not_detected  not_detected    not_detected   \n",
       "5                         NaN           NaN           NaN             NaN   \n",
       "6                         NaN           NaN           NaN             NaN   \n",
       "7                         NaN           NaN           NaN             NaN   \n",
       "8                not_detected  not_detected  not_detected    not_detected   \n",
       "9                not_detected  not_detected  not_detected    not_detected   \n",
       "\n",
       "  CoronavirusNL63 Rhinovirus/Enterovirus  Mycoplasma pneumoniae  \\\n",
       "0             NaN                    NaN                    NaN   \n",
       "1    not_detected               detected                    NaN   \n",
       "2             NaN                    NaN                    NaN   \n",
       "3             NaN                    NaN                    NaN   \n",
       "4    not_detected               detected                    NaN   \n",
       "5             NaN                    NaN                    NaN   \n",
       "6             NaN                    NaN                    NaN   \n",
       "7             NaN                    NaN                    NaN   \n",
       "8    not_detected           not_detected                    NaN   \n",
       "9    not_detected           not_detected                    NaN   \n",
       "\n",
       "  Coronavirus HKU1 Parainfluenza 3 Chlamydophila pneumoniae    Adenovirus  \\\n",
       "0              NaN             NaN                      NaN           NaN   \n",
       "1     not_detected    not_detected             not_detected  not_detected   \n",
       "2              NaN             NaN                      NaN           NaN   \n",
       "3              NaN             NaN                      NaN           NaN   \n",
       "4     not_detected    not_detected             not_detected  not_detected   \n",
       "5              NaN             NaN                      NaN           NaN   \n",
       "6              NaN             NaN                      NaN           NaN   \n",
       "7              NaN             NaN                      NaN           NaN   \n",
       "8     not_detected    not_detected             not_detected  not_detected   \n",
       "9     not_detected    not_detected             not_detected  not_detected   \n",
       "\n",
       "  Parainfluenza 4 Coronavirus229E CoronavirusOC43 Inf A H1N1 2009  \\\n",
       "0             NaN             NaN             NaN             NaN   \n",
       "1    not_detected    not_detected    not_detected    not_detected   \n",
       "2             NaN             NaN             NaN             NaN   \n",
       "3             NaN             NaN             NaN             NaN   \n",
       "4    not_detected    not_detected    not_detected    not_detected   \n",
       "5             NaN             NaN             NaN             NaN   \n",
       "6             NaN             NaN             NaN             NaN   \n",
       "7             NaN             NaN             NaN             NaN   \n",
       "8    not_detected    not_detected    not_detected    not_detected   \n",
       "9    not_detected    not_detected    not_detected    not_detected   \n",
       "\n",
       "  Bordetella pertussis Metapneumovirus Parainfluenza 2  Neutrophils      Urea  \\\n",
       "0                  NaN             NaN             NaN          NaN       NaN   \n",
       "1         not_detected    not_detected    not_detected    -0.619086  1.198059   \n",
       "2                  NaN             NaN             NaN          NaN       NaN   \n",
       "3                  NaN             NaN             NaN          NaN       NaN   \n",
       "4         not_detected    not_detected    not_detected          NaN       NaN   \n",
       "5                  NaN             NaN             NaN          NaN       NaN   \n",
       "6                  NaN             NaN             NaN          NaN       NaN   \n",
       "7                  NaN             NaN             NaN          NaN       NaN   \n",
       "8         not_detected    not_detected    not_detected    -0.127395 -0.067309   \n",
       "9         not_detected    not_detected    not_detected          NaN       NaN   \n",
       "\n",
       "   Proteina C reativa mg/dL  Creatinine  Potassium    Sodium  \\\n",
       "0                       NaN         NaN        NaN       NaN   \n",
       "1                 -0.147895    2.089928  -0.305787  0.862512   \n",
       "2                       NaN         NaN        NaN       NaN   \n",
       "3                       NaN         NaN        NaN       NaN   \n",
       "4                       NaN         NaN        NaN       NaN   \n",
       "5                       NaN         NaN        NaN       NaN   \n",
       "6                       NaN         NaN        NaN       NaN   \n",
       "7                       NaN         NaN        NaN       NaN   \n",
       "8                 -0.286986   -1.838623   0.930020  0.503132   \n",
       "9                       NaN         NaN        NaN       NaN   \n",
       "\n",
       "  Influenza B, rapid test Influenza A, rapid test  Alanine transaminase  \\\n",
       "0                     NaN                     NaN                   NaN   \n",
       "1                negative                negative                   NaN   \n",
       "2                     NaN                     NaN                   NaN   \n",
       "3                     NaN                     NaN                   NaN   \n",
       "4                     NaN                     NaN                   NaN   \n",
       "5                     NaN                     NaN                   NaN   \n",
       "6                     NaN                     NaN                   NaN   \n",
       "7                     NaN                     NaN                   NaN   \n",
       "8                     NaN                     NaN             -0.586821   \n",
       "9                     NaN                     NaN                   NaN   \n",
       "\n",
       "   Aspartate transaminase  Gamma-glutamyltransferase   Total Bilirubin  \\\n",
       "0                     NaN                         NaN              NaN   \n",
       "1                     NaN                         NaN              NaN   \n",
       "2                     NaN                         NaN              NaN   \n",
       "3                     NaN                         NaN              NaN   \n",
       "4                     NaN                         NaN              NaN   \n",
       "5                     NaN                         NaN              NaN   \n",
       "6                     NaN                         NaN              NaN   \n",
       "7                     NaN                         NaN              NaN   \n",
       "8                 -0.1622                         NaN              NaN   \n",
       "9                     NaN                         NaN              NaN   \n",
       "\n",
       "   Direct Bilirubin  Indirect Bilirubin  Alkaline phosphatase  \\\n",
       "0               NaN                 NaN                   NaN   \n",
       "1               NaN                 NaN                   NaN   \n",
       "2               NaN                 NaN                   NaN   \n",
       "3               NaN                 NaN                   NaN   \n",
       "4               NaN                 NaN                   NaN   \n",
       "5               NaN                 NaN                   NaN   \n",
       "6               NaN                 NaN                   NaN   \n",
       "7               NaN                 NaN                   NaN   \n",
       "8               NaN                 NaN                   NaN   \n",
       "9               NaN                 NaN                   NaN   \n",
       "\n",
       "   Ionized calcium  Strepto A  Magnesium  pCO2 (venous blood gas analysis)  \\\n",
       "0               NaN       NaN        NaN                               NaN   \n",
       "1               NaN       NaN        NaN                               NaN   \n",
       "2               NaN       NaN        NaN                               NaN   \n",
       "3               NaN       NaN        NaN                               NaN   \n",
       "4               NaN       NaN        NaN                               NaN   \n",
       "5               NaN       NaN        NaN                               NaN   \n",
       "6               NaN       NaN        NaN                               NaN   \n",
       "7               NaN       NaN        NaN                               NaN   \n",
       "8          0.724353       NaN   1.075153                          0.615594   \n",
       "9               NaN       NaN        NaN                               NaN   \n",
       "\n",
       "   Hb saturation (venous blood gas analysis)  \\\n",
       "0                                        NaN   \n",
       "1                                        NaN   \n",
       "2                                        NaN   \n",
       "3                                        NaN   \n",
       "4                                        NaN   \n",
       "5                                        NaN   \n",
       "6                                        NaN   \n",
       "7                                        NaN   \n",
       "8                                  -0.554737   \n",
       "9                                        NaN   \n",
       "\n",
       "   Base excess (venous blood gas analysis)  pO2 (venous blood gas analysis)  \\\n",
       "0                                      NaN                              NaN   \n",
       "1                                      NaN                              NaN   \n",
       "2                                      NaN                              NaN   \n",
       "3                                      NaN                              NaN   \n",
       "4                                      NaN                              NaN   \n",
       "5                                      NaN                              NaN   \n",
       "6                                      NaN                              NaN   \n",
       "7                                      NaN                              NaN   \n",
       "8                                -0.283748                        -0.562902   \n",
       "9                                      NaN                              NaN   \n",
       "\n",
       "   Fio2 (venous blood gas analysis)  Total CO2 (venous blood gas analysis)  \\\n",
       "0                               NaN                                    NaN   \n",
       "1                               NaN                                    NaN   \n",
       "2                               NaN                                    NaN   \n",
       "3                               NaN                                    NaN   \n",
       "4                               NaN                                    NaN   \n",
       "5                               NaN                                    NaN   \n",
       "6                               NaN                                    NaN   \n",
       "7                               NaN                                    NaN   \n",
       "8                               NaN                               0.104088   \n",
       "9                               NaN                                    NaN   \n",
       "\n",
       "   pH (venous blood gas analysis)  HCO3 (venous blood gas analysis)  Rods #  \\\n",
       "0                             NaN                               NaN     NaN   \n",
       "1                             NaN                               NaN     NaN   \n",
       "2                             NaN                               NaN     NaN   \n",
       "3                             NaN                               NaN     NaN   \n",
       "4                             NaN                               NaN     NaN   \n",
       "5                             NaN                               NaN     NaN   \n",
       "6                             NaN                               NaN     NaN   \n",
       "7                             NaN                               NaN     NaN   \n",
       "8                       -0.855513                          0.036345     NaN   \n",
       "9                             NaN                               NaN     NaN   \n",
       "\n",
       "   Segmented  Promyelocytes  Metamyelocytes  Myelocytes  Myeloblasts  \\\n",
       "0        NaN            NaN             NaN         NaN          NaN   \n",
       "1        NaN            NaN             NaN         NaN          NaN   \n",
       "2        NaN            NaN             NaN         NaN          NaN   \n",
       "3        NaN            NaN             NaN         NaN          NaN   \n",
       "4        NaN            NaN             NaN         NaN          NaN   \n",
       "5        NaN            NaN             NaN         NaN          NaN   \n",
       "6        NaN            NaN             NaN         NaN          NaN   \n",
       "7        NaN            NaN             NaN         NaN          NaN   \n",
       "8        NaN            NaN             NaN         NaN          NaN   \n",
       "9        NaN            NaN             NaN         NaN          NaN   \n",
       "\n",
       "  Urine - Esterase Urine - Aspect Urine - pH Urine - Hemoglobin  \\\n",
       "0              NaN            NaN        NaN                NaN   \n",
       "1              NaN            NaN        NaN                NaN   \n",
       "2              NaN            NaN        NaN                NaN   \n",
       "3              NaN            NaN        NaN                NaN   \n",
       "4              NaN            NaN        NaN                NaN   \n",
       "5              NaN            NaN        NaN                NaN   \n",
       "6              NaN            NaN        NaN                NaN   \n",
       "7              NaN            NaN        NaN                NaN   \n",
       "8              NaN            NaN        NaN                NaN   \n",
       "9              NaN            NaN        NaN                NaN   \n",
       "\n",
       "  Urine - Bile pigments Urine - Ketone Bodies Urine - Nitrite  \\\n",
       "0                   NaN                   NaN             NaN   \n",
       "1                   NaN                   NaN             NaN   \n",
       "2                   NaN                   NaN             NaN   \n",
       "3                   NaN                   NaN             NaN   \n",
       "4                   NaN                   NaN             NaN   \n",
       "5                   NaN                   NaN             NaN   \n",
       "6                   NaN                   NaN             NaN   \n",
       "7                   NaN                   NaN             NaN   \n",
       "8                   NaN                   NaN             NaN   \n",
       "9                   NaN                   NaN             NaN   \n",
       "\n",
       "   Urine - Density Urine - Urobilinogen Urine - Protein  Urine - Sugar  \\\n",
       "0              NaN                  NaN             NaN            NaN   \n",
       "1              NaN                  NaN             NaN            NaN   \n",
       "2              NaN                  NaN             NaN            NaN   \n",
       "3              NaN                  NaN             NaN            NaN   \n",
       "4              NaN                  NaN             NaN            NaN   \n",
       "5              NaN                  NaN             NaN            NaN   \n",
       "6              NaN                  NaN             NaN            NaN   \n",
       "7              NaN                  NaN             NaN            NaN   \n",
       "8              NaN                  NaN             NaN            NaN   \n",
       "9              NaN                  NaN             NaN            NaN   \n",
       "\n",
       "  Urine - Leukocytes Urine - Crystals  Urine - Red blood cells  \\\n",
       "0                NaN              NaN                      NaN   \n",
       "1                NaN              NaN                      NaN   \n",
       "2                NaN              NaN                      NaN   \n",
       "3                NaN              NaN                      NaN   \n",
       "4                NaN              NaN                      NaN   \n",
       "5                NaN              NaN                      NaN   \n",
       "6                NaN              NaN                      NaN   \n",
       "7                NaN              NaN                      NaN   \n",
       "8                NaN              NaN                      NaN   \n",
       "9                NaN              NaN                      NaN   \n",
       "\n",
       "  Urine - Hyaline cylinders Urine - Granular cylinders Urine - Yeasts  \\\n",
       "0                       NaN                        NaN            NaN   \n",
       "1                       NaN                        NaN            NaN   \n",
       "2                       NaN                        NaN            NaN   \n",
       "3                       NaN                        NaN            NaN   \n",
       "4                       NaN                        NaN            NaN   \n",
       "5                       NaN                        NaN            NaN   \n",
       "6                       NaN                        NaN            NaN   \n",
       "7                       NaN                        NaN            NaN   \n",
       "8                       NaN                        NaN            NaN   \n",
       "9                       NaN                        NaN            NaN   \n",
       "\n",
       "  Urine - Color  Partial thromboplastin time (PTT)   \\\n",
       "0           NaN                                 NaN   \n",
       "1           NaN                                 NaN   \n",
       "2           NaN                                 NaN   \n",
       "3           NaN                                 NaN   \n",
       "4           NaN                                 NaN   \n",
       "5           NaN                                 NaN   \n",
       "6           NaN                                 NaN   \n",
       "7           NaN                                 NaN   \n",
       "8           NaN                                 NaN   \n",
       "9           NaN                                 NaN   \n",
       "\n",
       "   Relationship (Patient/Normal)  International normalized ratio (INR)  \\\n",
       "0                            NaN                                   NaN   \n",
       "1                            NaN                                   NaN   \n",
       "2                            NaN                                   NaN   \n",
       "3                            NaN                                   NaN   \n",
       "4                            NaN                                   NaN   \n",
       "5                            NaN                                   NaN   \n",
       "6                            NaN                                   NaN   \n",
       "7                            NaN                                   NaN   \n",
       "8                      -0.089481                              0.296546   \n",
       "9                            NaN                                   NaN   \n",
       "\n",
       "   Lactic Dehydrogenase  Prothrombin time (PT), Activity  Vitamin B12  \\\n",
       "0                   NaN                              NaN          NaN   \n",
       "1                   NaN                              NaN          NaN   \n",
       "2                   NaN                              NaN          NaN   \n",
       "3                   NaN                              NaN          NaN   \n",
       "4                   NaN                              NaN          NaN   \n",
       "5                   NaN                              NaN          NaN   \n",
       "6                   NaN                              NaN          NaN   \n",
       "7                   NaN                              NaN          NaN   \n",
       "8              0.907723                              NaN          NaN   \n",
       "9                   NaN                              NaN          NaN   \n",
       "\n",
       "   Creatine phosphokinase (CPK)   Ferritin  Arterial Lactic Acid  \\\n",
       "0                            NaN       NaN                   NaN   \n",
       "1                            NaN       NaN                   NaN   \n",
       "2                            NaN       NaN                   NaN   \n",
       "3                            NaN       NaN                   NaN   \n",
       "4                            NaN       NaN                   NaN   \n",
       "5                            NaN       NaN                   NaN   \n",
       "6                            NaN       NaN                   NaN   \n",
       "7                            NaN       NaN                   NaN   \n",
       "8                      -0.267856       NaN                   NaN   \n",
       "9                            NaN       NaN                   NaN   \n",
       "\n",
       "   Lipase dosage  D-Dimer  Albumin  Hb saturation (arterial blood gases)  \\\n",
       "0            NaN      NaN      NaN                                   NaN   \n",
       "1            NaN      NaN      NaN                                   NaN   \n",
       "2            NaN      NaN      NaN                                   NaN   \n",
       "3            NaN      NaN      NaN                                   NaN   \n",
       "4            NaN      NaN      NaN                                   NaN   \n",
       "5            NaN      NaN      NaN                                   NaN   \n",
       "6            NaN      NaN      NaN                                   NaN   \n",
       "7            NaN      NaN      NaN                                   NaN   \n",
       "8            NaN      NaN      NaN                                   NaN   \n",
       "9            NaN      NaN      NaN                                   NaN   \n",
       "\n",
       "   pCO2 (arterial blood gas analysis)  \\\n",
       "0                                 NaN   \n",
       "1                                 NaN   \n",
       "2                                 NaN   \n",
       "3                                 NaN   \n",
       "4                                 NaN   \n",
       "5                                 NaN   \n",
       "6                                 NaN   \n",
       "7                                 NaN   \n",
       "8                                 NaN   \n",
       "9                                 NaN   \n",
       "\n",
       "   Base excess (arterial blood gas analysis)  \\\n",
       "0                                        NaN   \n",
       "1                                        NaN   \n",
       "2                                        NaN   \n",
       "3                                        NaN   \n",
       "4                                        NaN   \n",
       "5                                        NaN   \n",
       "6                                        NaN   \n",
       "7                                        NaN   \n",
       "8                                        NaN   \n",
       "9                                        NaN   \n",
       "\n",
       "   pH (arterial blood gas analysis)  Total CO2 (arterial blood gas analysis)  \\\n",
       "0                               NaN                                      NaN   \n",
       "1                               NaN                                      NaN   \n",
       "2                               NaN                                      NaN   \n",
       "3                               NaN                                      NaN   \n",
       "4                               NaN                                      NaN   \n",
       "5                               NaN                                      NaN   \n",
       "6                               NaN                                      NaN   \n",
       "7                               NaN                                      NaN   \n",
       "8                               NaN                                      NaN   \n",
       "9                               NaN                                      NaN   \n",
       "\n",
       "   HCO3 (arterial blood gas analysis)  pO2 (arterial blood gas analysis)  \\\n",
       "0                                 NaN                                NaN   \n",
       "1                                 NaN                                NaN   \n",
       "2                                 NaN                                NaN   \n",
       "3                                 NaN                                NaN   \n",
       "4                                 NaN                                NaN   \n",
       "5                                 NaN                                NaN   \n",
       "6                                 NaN                                NaN   \n",
       "7                                 NaN                                NaN   \n",
       "8                                 NaN                                NaN   \n",
       "9                                 NaN                                NaN   \n",
       "\n",
       "   Arteiral Fio2  Phosphor  ctO2 (arterial blood gas analysis)  \n",
       "0            NaN       NaN                                 NaN  \n",
       "1            NaN       NaN                                 NaN  \n",
       "2            NaN       NaN                                 NaN  \n",
       "3            NaN       NaN                                 NaN  \n",
       "4            NaN       NaN                                 NaN  \n",
       "5            NaN       NaN                                 NaN  \n",
       "6            NaN       NaN                                 NaN  \n",
       "7            NaN       NaN                                 NaN  \n",
       "8            NaN  0.730393                                 NaN  \n",
       "9            NaN       NaN                                 NaN  "
      ]
     },
     "execution_count": 204,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 205,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(5644, 111)"
      ]
     },
     "execution_count": 205,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 206,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Patient ID', 'Patient age quantile', 'SARS-Cov-2 exam result',\n",
       "       'Patient addmited to regular ward (1=yes, 0=no)',\n",
       "       'Patient addmited to semi-intensive unit (1=yes, 0=no)',\n",
       "       'Patient addmited to intensive care unit (1=yes, 0=no)', 'Hematocrit',\n",
       "       'Hemoglobin', 'Platelets', 'Mean platelet volume ',\n",
       "       ...\n",
       "       'Hb saturation (arterial blood gases)',\n",
       "       'pCO2 (arterial blood gas analysis)',\n",
       "       'Base excess (arterial blood gas analysis)',\n",
       "       'pH (arterial blood gas analysis)',\n",
       "       'Total CO2 (arterial blood gas analysis)',\n",
       "       'HCO3 (arterial blood gas analysis)',\n",
       "       'pO2 (arterial blood gas analysis)', 'Arteiral Fio2', 'Phosphor',\n",
       "       'ctO2 (arterial blood gas analysis)'],\n",
       "      dtype='object', length=111)"
      ]
     },
     "execution_count": 206,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 207,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Urine - Sugar                                            5644\n",
       "Mycoplasma pneumoniae                                    5644\n",
       "Partial thromboplastin time (PTT)                        5644\n",
       "Prothrombin time (PT), Activity                          5644\n",
       "D-Dimer                                                  5644\n",
       "Fio2 (venous blood gas analysis)                         5643\n",
       "Urine - Nitrite                                          5643\n",
       "Vitamin B12                                              5641\n",
       "Lipase dosage                                            5636\n",
       "Albumin                                                  5631\n",
       "Phosphor                                                 5624\n",
       "Arteiral Fio2                                            5624\n",
       "Ferritin                                                 5621\n",
       "Arterial Lactic Acid                                     5617\n",
       "ctO2 (arterial blood gas analysis)                       5617\n",
       "Hb saturation (arterial blood gases)                     5617\n",
       "Total CO2 (arterial blood gas analysis)                  5617\n",
       "pCO2 (arterial blood gas analysis)                       5617\n",
       "Base excess (arterial blood gas analysis)                5617\n",
       "pO2 (arterial blood gas analysis)                        5617\n",
       "HCO3 (arterial blood gas analysis)                       5617\n",
       "pH (arterial blood gas analysis)                         5617\n",
       "Magnesium                                                5604\n",
       "Ionized calcium                                          5594\n",
       "Urine - Ketone Bodies                                    5587\n",
       "Urine - Protein                                          5584\n",
       "Urine - Esterase                                         5584\n",
       "Urine - Hyaline cylinders                                5577\n",
       "Urine - Granular cylinders                               5575\n",
       "Urine - Urobilinogen                                     5575\n",
       "Urine - Hemoglobin                                       5574\n",
       "Urine - Bile pigments                                    5574\n",
       "Urine - Density                                          5574\n",
       "Urine - Aspect                                           5574\n",
       "Urine - pH                                               5574\n",
       "Urine - Crystals                                         5574\n",
       "Urine - Red blood cells                                  5574\n",
       "Urine - Yeasts                                           5574\n",
       "Urine - Leukocytes                                       5574\n",
       "Urine - Color                                            5574\n",
       "Relationship (Patient/Normal)                            5553\n",
       "Rods #                                                   5547\n",
       "Myelocytes                                               5547\n",
       "Promyelocytes                                            5547\n",
       "Metamyelocytes                                           5547\n",
       "Myeloblasts                                              5547\n",
       "Segmented                                                5547\n",
       "Lactic Dehydrogenase                                     5543\n",
       "Creatine phosphokinase (CPK)                             5540\n",
       "International normalized ratio (INR)                     5511\n",
       "pCO2 (venous blood gas analysis)                         5508\n",
       "pH (venous blood gas analysis)                           5508\n",
       "Total CO2 (venous blood gas analysis)                    5508\n",
       "pO2 (venous blood gas analysis)                          5508\n",
       "Base excess (venous blood gas analysis)                  5508\n",
       "Hb saturation (venous blood gas analysis)                5508\n",
       "HCO3 (venous blood gas analysis)                         5508\n",
       "Alkaline phosphatase                                     5500\n",
       "Gamma-glutamyltransferase                                5491\n",
       "Indirect Bilirubin                                       5462\n",
       "Direct Bilirubin                                         5462\n",
       "Total Bilirubin                                          5462\n",
       "Serum Glucose                                            5436\n",
       "Alanine transaminase                                     5419\n",
       "Aspartate transaminase                                   5418\n",
       "Strepto A                                                5312\n",
       "Sodium                                                   5274\n",
       "Potassium                                                5273\n",
       "Urea                                                     5247\n",
       "Creatinine                                               5220\n",
       "Proteina C reativa mg/dL                                 5138\n",
       "Neutrophils                                              5131\n",
       "Mean platelet volume                                     5045\n",
       "Monocytes                                                5043\n",
       "Platelets                                                5042\n",
       "Lymphocytes                                              5042\n",
       "Mean corpuscular hemoglobin (MCH)                        5042\n",
       "Basophils                                                5042\n",
       "Leukocytes                                               5042\n",
       "Mean corpuscular hemoglobin concentration (MCHC)         5042\n",
       "Eosinophils                                              5042\n",
       "Red blood Cells                                          5042\n",
       "Red blood cell distribution width (RDW)                  5042\n",
       "Mean corpuscular volume (MCV)                            5042\n",
       "Hematocrit                                               5041\n",
       "Hemoglobin                                               5041\n",
       "Influenza A, rapid test                                  4824\n",
       "Influenza B, rapid test                                  4824\n",
       "Parainfluenza 1                                          4292\n",
       "Rhinovirus/Enterovirus                                   4292\n",
       "Adenovirus                                               4292\n",
       "Inf A H1N1 2009                                          4292\n",
       "Parainfluenza 2                                          4292\n",
       "CoronavirusNL63                                          4292\n",
       "Metapneumovirus                                          4292\n",
       "Coronavirus HKU1                                         4292\n",
       "Parainfluenza 3                                          4292\n",
       "Chlamydophila pneumoniae                                 4292\n",
       "Bordetella pertussis                                     4292\n",
       "Parainfluenza 4                                          4292\n",
       "Coronavirus229E                                          4292\n",
       "CoronavirusOC43                                          4292\n",
       "Influenza A                                              4290\n",
       "Respiratory Syncytial Virus                              4290\n",
       "Influenza B                                              4290\n",
       "Patient addmited to regular ward (1=yes, 0=no)              0\n",
       "SARS-Cov-2 exam result                                      0\n",
       "Patient age quantile                                        0\n",
       "Patient addmited to semi-intensive unit (1=yes, 0=no)       0\n",
       "Patient addmited to intensive care unit (1=yes, 0=no)       0\n",
       "Patient ID                                                  0\n",
       "dtype: int64"
      ]
     },
     "execution_count": 207,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_nan = df.isna().sum().sort_values(ascending=False)    \n",
    "df_nan"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Compute columns to drop"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 208,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(5644, 37)"
      ]
     },
     "execution_count": 208,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "drop_columns = df_nan.index[df_nan > 5042]\n",
    "df.drop(drop_columns, axis=1, inplace=True)\n",
    "df.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We drop a row if it contains 30% of values NaN"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 209,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(366, 37)"
      ]
     },
     "execution_count": 209,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = df.dropna(thresh=0.7 * len(df.columns))\n",
    "df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 210,
   "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>Patient ID</th>\n",
       "      <th>Patient age quantile</th>\n",
       "      <th>SARS-Cov-2 exam result</th>\n",
       "      <th>Patient addmited to regular ward (1=yes, 0=no)</th>\n",
       "      <th>Patient addmited to semi-intensive unit (1=yes, 0=no)</th>\n",
       "      <th>Patient addmited to intensive care unit (1=yes, 0=no)</th>\n",
       "      <th>Hematocrit</th>\n",
       "      <th>Hemoglobin</th>\n",
       "      <th>Platelets</th>\n",
       "      <th>Red blood Cells</th>\n",
       "      <th>Lymphocytes</th>\n",
       "      <th>Mean corpuscular hemoglobin concentration (MCHC)</th>\n",
       "      <th>Leukocytes</th>\n",
       "      <th>Basophils</th>\n",
       "      <th>Mean corpuscular hemoglobin (MCH)</th>\n",
       "      <th>Eosinophils</th>\n",
       "      <th>Mean corpuscular volume (MCV)</th>\n",
       "      <th>Red blood cell distribution width (RDW)</th>\n",
       "      <th>Respiratory Syncytial Virus</th>\n",
       "      <th>Influenza A</th>\n",
       "      <th>Influenza B</th>\n",
       "      <th>Parainfluenza 1</th>\n",
       "      <th>CoronavirusNL63</th>\n",
       "      <th>Rhinovirus/Enterovirus</th>\n",
       "      <th>Coronavirus HKU1</th>\n",
       "      <th>Parainfluenza 3</th>\n",
       "      <th>Chlamydophila pneumoniae</th>\n",
       "      <th>Adenovirus</th>\n",
       "      <th>Parainfluenza 4</th>\n",
       "      <th>Coronavirus229E</th>\n",
       "      <th>CoronavirusOC43</th>\n",
       "      <th>Inf A H1N1 2009</th>\n",
       "      <th>Bordetella pertussis</th>\n",
       "      <th>Metapneumovirus</th>\n",
       "      <th>Parainfluenza 2</th>\n",
       "      <th>Influenza B, rapid test</th>\n",
       "      <th>Influenza A, rapid test</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>126e9dd13932f68</td>\n",
       "      <td>17</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.236515</td>\n",
       "      <td>-0.022340</td>\n",
       "      <td>-0.517413</td>\n",
       "      <td>0.102004</td>\n",
       "      <td>0.318366</td>\n",
       "      <td>-0.950790</td>\n",
       "      <td>-0.094610</td>\n",
       "      <td>-0.223767</td>\n",
       "      <td>-0.292269</td>\n",
       "      <td>1.482158</td>\n",
       "      <td>0.166192</td>\n",
       "      <td>-0.625073</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>negative</td>\n",
       "      <td>negative</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>8bb9d64f0215244</td>\n",
       "      <td>1</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>-1.571682</td>\n",
       "      <td>-0.774212</td>\n",
       "      <td>1.429667</td>\n",
       "      <td>-0.850035</td>\n",
       "      <td>-0.005738</td>\n",
       "      <td>3.331071</td>\n",
       "      <td>0.364550</td>\n",
       "      <td>-0.223767</td>\n",
       "      <td>0.178175</td>\n",
       "      <td>1.018625</td>\n",
       "      <td>-1.336024</td>\n",
       "      <td>-0.978899</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>6c9d3323975b082</td>\n",
       "      <td>9</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-0.747693</td>\n",
       "      <td>-0.586244</td>\n",
       "      <td>-0.429480</td>\n",
       "      <td>-1.361315</td>\n",
       "      <td>-1.114514</td>\n",
       "      <td>0.542882</td>\n",
       "      <td>-0.884923</td>\n",
       "      <td>0.081693</td>\n",
       "      <td>1.746323</td>\n",
       "      <td>-0.666950</td>\n",
       "      <td>1.668409</td>\n",
       "      <td>-1.067355</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>negative</td>\n",
       "      <td>positive</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>d3ea751f3db9de9</td>\n",
       "      <td>11</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.991838</td>\n",
       "      <td>0.792188</td>\n",
       "      <td>0.072992</td>\n",
       "      <td>0.542763</td>\n",
       "      <td>0.045436</td>\n",
       "      <td>-0.452899</td>\n",
       "      <td>-0.211488</td>\n",
       "      <td>-0.834685</td>\n",
       "      <td>0.334989</td>\n",
       "      <td>-0.709090</td>\n",
       "      <td>0.606842</td>\n",
       "      <td>0.171035</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>fc41531ca4faf1e</td>\n",
       "      <td>13</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.014726</td>\n",
       "      <td>0.854844</td>\n",
       "      <td>-0.178244</td>\n",
       "      <td>0.489872</td>\n",
       "      <td>-0.730707</td>\n",
       "      <td>-0.353319</td>\n",
       "      <td>-0.075131</td>\n",
       "      <td>2.525365</td>\n",
       "      <td>0.544077</td>\n",
       "      <td>0.217977</td>\n",
       "      <td>0.767079</td>\n",
       "      <td>0.171035</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>891d0f6449ff3d7</td>\n",
       "      <td>14</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.740064</td>\n",
       "      <td>0.854844</td>\n",
       "      <td>0.361914</td>\n",
       "      <td>0.436981</td>\n",
       "      <td>-0.227493</td>\n",
       "      <td>0.642463</td>\n",
       "      <td>0.105751</td>\n",
       "      <td>-0.529226</td>\n",
       "      <td>0.596348</td>\n",
       "      <td>-0.371974</td>\n",
       "      <td>0.386517</td>\n",
       "      <td>-0.713529</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>30</th>\n",
       "      <td>ebdd7c67fcb21b4</td>\n",
       "      <td>9</td>\n",
       "      <td>negative</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-0.679027</td>\n",
       "      <td>-0.711556</td>\n",
       "      <td>0.952319</td>\n",
       "      <td>-0.321124</td>\n",
       "      <td>-0.875701</td>\n",
       "      <td>-0.253742</td>\n",
       "      <td>-0.286623</td>\n",
       "      <td>-0.223767</td>\n",
       "      <td>-0.710443</td>\n",
       "      <td>-0.540532</td>\n",
       "      <td>-0.675050</td>\n",
       "      <td>-0.890442</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>negative</td>\n",
       "      <td>negative</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>32</th>\n",
       "      <td>296adf066a9bf03</td>\n",
       "      <td>8</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.236515</td>\n",
       "      <td>0.040316</td>\n",
       "      <td>0.072992</td>\n",
       "      <td>0.066744</td>\n",
       "      <td>1.239503</td>\n",
       "      <td>-0.652057</td>\n",
       "      <td>-0.545423</td>\n",
       "      <td>0.998070</td>\n",
       "      <td>-0.083183</td>\n",
       "      <td>0.133698</td>\n",
       "      <td>0.246311</td>\n",
       "      <td>-0.094334</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>34</th>\n",
       "      <td>0b1e43c5e3fb1d1</td>\n",
       "      <td>17</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.808730</td>\n",
       "      <td>1.042812</td>\n",
       "      <td>-0.278739</td>\n",
       "      <td>0.701437</td>\n",
       "      <td>-0.261609</td>\n",
       "      <td>1.040773</td>\n",
       "      <td>0.000005</td>\n",
       "      <td>0.387152</td>\n",
       "      <td>0.439533</td>\n",
       "      <td>0.049419</td>\n",
       "      <td>-0.014074</td>\n",
       "      <td>-0.094334</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50</th>\n",
       "      <td>11e4956b770f080</td>\n",
       "      <td>17</td>\n",
       "      <td>negative</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.014726</td>\n",
       "      <td>0.666876</td>\n",
       "      <td>-0.203368</td>\n",
       "      <td>0.295938</td>\n",
       "      <td>-0.261609</td>\n",
       "      <td>-0.950790</td>\n",
       "      <td>-0.083479</td>\n",
       "      <td>-0.223767</td>\n",
       "      <td>0.544077</td>\n",
       "      <td>0.133698</td>\n",
       "      <td>1.167670</td>\n",
       "      <td>-0.359703</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>not_detected</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "         Patient ID  Patient age quantile SARS-Cov-2 exam result  \\\n",
       "1   126e9dd13932f68                    17               negative   \n",
       "8   8bb9d64f0215244                     1               negative   \n",
       "15  6c9d3323975b082                     9               negative   \n",
       "18  d3ea751f3db9de9                    11               negative   \n",
       "28  fc41531ca4faf1e                    13               negative   \n",
       "29  891d0f6449ff3d7                    14               negative   \n",
       "30  ebdd7c67fcb21b4                     9               negative   \n",
       "32  296adf066a9bf03                     8               negative   \n",
       "34  0b1e43c5e3fb1d1                    17               negative   \n",
       "50  11e4956b770f080                    17               negative   \n",
       "\n",
       "    Patient addmited to regular ward (1=yes, 0=no)  \\\n",
       "1                                                0   \n",
       "8                                                0   \n",
       "15                                               0   \n",
       "18                                               0   \n",
       "28                                               0   \n",
       "29                                               0   \n",
       "30                                               1   \n",
       "32                                               0   \n",
       "34                                               0   \n",
       "50                                               0   \n",
       "\n",
       "    Patient addmited to semi-intensive unit (1=yes, 0=no)  \\\n",
       "1                                                   0       \n",
       "8                                                   1       \n",
       "15                                                  0       \n",
       "18                                                  0       \n",
       "28                                                  0       \n",
       "29                                                  0       \n",
       "30                                                  0       \n",
       "32                                                  0       \n",
       "34                                                  0       \n",
       "50                                                  0       \n",
       "\n",
       "    Patient addmited to intensive care unit (1=yes, 0=no)  Hematocrit  \\\n",
       "1                                                   0        0.236515   \n",
       "8                                                   0       -1.571682   \n",
       "15                                                  0       -0.747693   \n",
       "18                                                  0        0.991838   \n",
       "28                                                  0        1.014726   \n",
       "29                                                  0        0.740064   \n",
       "30                                                  0       -0.679027   \n",
       "32                                                  0        0.236515   \n",
       "34                                                  0        0.808730   \n",
       "50                                                  0        1.014726   \n",
       "\n",
       "    Hemoglobin  Platelets  Red blood Cells  Lymphocytes  \\\n",
       "1    -0.022340  -0.517413         0.102004     0.318366   \n",
       "8    -0.774212   1.429667        -0.850035    -0.005738   \n",
       "15   -0.586244  -0.429480        -1.361315    -1.114514   \n",
       "18    0.792188   0.072992         0.542763     0.045436   \n",
       "28    0.854844  -0.178244         0.489872    -0.730707   \n",
       "29    0.854844   0.361914         0.436981    -0.227493   \n",
       "30   -0.711556   0.952319        -0.321124    -0.875701   \n",
       "32    0.040316   0.072992         0.066744     1.239503   \n",
       "34    1.042812  -0.278739         0.701437    -0.261609   \n",
       "50    0.666876  -0.203368         0.295938    -0.261609   \n",
       "\n",
       "    Mean corpuscular hemoglobin concentration (MCHC)  Leukocytes  Basophils  \\\n",
       "1                                          -0.950790   -0.094610  -0.223767   \n",
       "8                                           3.331071    0.364550  -0.223767   \n",
       "15                                          0.542882   -0.884923   0.081693   \n",
       "18                                         -0.452899   -0.211488  -0.834685   \n",
       "28                                         -0.353319   -0.075131   2.525365   \n",
       "29                                          0.642463    0.105751  -0.529226   \n",
       "30                                         -0.253742   -0.286623  -0.223767   \n",
       "32                                         -0.652057   -0.545423   0.998070   \n",
       "34                                          1.040773    0.000005   0.387152   \n",
       "50                                         -0.950790   -0.083479  -0.223767   \n",
       "\n",
       "    Mean corpuscular hemoglobin (MCH)  Eosinophils  \\\n",
       "1                           -0.292269     1.482158   \n",
       "8                            0.178175     1.018625   \n",
       "15                           1.746323    -0.666950   \n",
       "18                           0.334989    -0.709090   \n",
       "28                           0.544077     0.217977   \n",
       "29                           0.596348    -0.371974   \n",
       "30                          -0.710443    -0.540532   \n",
       "32                          -0.083183     0.133698   \n",
       "34                           0.439533     0.049419   \n",
       "50                           0.544077     0.133698   \n",
       "\n",
       "    Mean corpuscular volume (MCV)  Red blood cell distribution width (RDW)  \\\n",
       "1                        0.166192                                -0.625073   \n",
       "8                       -1.336024                                -0.978899   \n",
       "15                       1.668409                                -1.067355   \n",
       "18                       0.606842                                 0.171035   \n",
       "28                       0.767079                                 0.171035   \n",
       "29                       0.386517                                -0.713529   \n",
       "30                      -0.675050                                -0.890442   \n",
       "32                       0.246311                                -0.094334   \n",
       "34                      -0.014074                                -0.094334   \n",
       "50                       1.167670                                -0.359703   \n",
       "\n",
       "   Respiratory Syncytial Virus   Influenza A   Influenza B Parainfluenza 1  \\\n",
       "1                 not_detected  not_detected  not_detected    not_detected   \n",
       "8                 not_detected  not_detected  not_detected    not_detected   \n",
       "15                not_detected  not_detected  not_detected    not_detected   \n",
       "18                not_detected  not_detected  not_detected    not_detected   \n",
       "28                not_detected  not_detected  not_detected    not_detected   \n",
       "29                not_detected  not_detected  not_detected    not_detected   \n",
       "30                not_detected  not_detected      detected    not_detected   \n",
       "32                not_detected  not_detected  not_detected    not_detected   \n",
       "34                not_detected  not_detected  not_detected    not_detected   \n",
       "50                not_detected  not_detected  not_detected    not_detected   \n",
       "\n",
       "   CoronavirusNL63 Rhinovirus/Enterovirus Coronavirus HKU1 Parainfluenza 3  \\\n",
       "1     not_detected               detected     not_detected    not_detected   \n",
       "8     not_detected           not_detected     not_detected    not_detected   \n",
       "15    not_detected           not_detected     not_detected    not_detected   \n",
       "18    not_detected               detected     not_detected    not_detected   \n",
       "28    not_detected               detected     not_detected    not_detected   \n",
       "29    not_detected           not_detected     not_detected    not_detected   \n",
       "30    not_detected           not_detected     not_detected    not_detected   \n",
       "32    not_detected           not_detected     not_detected    not_detected   \n",
       "34    not_detected               detected     not_detected    not_detected   \n",
       "50        detected           not_detected     not_detected    not_detected   \n",
       "\n",
       "   Chlamydophila pneumoniae    Adenovirus Parainfluenza 4 Coronavirus229E  \\\n",
       "1              not_detected  not_detected    not_detected    not_detected   \n",
       "8              not_detected  not_detected    not_detected    not_detected   \n",
       "15             not_detected  not_detected    not_detected    not_detected   \n",
       "18             not_detected  not_detected    not_detected    not_detected   \n",
       "28             not_detected  not_detected    not_detected    not_detected   \n",
       "29             not_detected  not_detected    not_detected    not_detected   \n",
       "30             not_detected  not_detected    not_detected    not_detected   \n",
       "32             not_detected  not_detected    not_detected    not_detected   \n",
       "34             not_detected  not_detected    not_detected    not_detected   \n",
       "50             not_detected  not_detected    not_detected    not_detected   \n",
       "\n",
       "   CoronavirusOC43 Inf A H1N1 2009 Bordetella pertussis Metapneumovirus  \\\n",
       "1     not_detected    not_detected         not_detected    not_detected   \n",
       "8     not_detected    not_detected         not_detected    not_detected   \n",
       "15    not_detected        detected         not_detected    not_detected   \n",
       "18    not_detected    not_detected         not_detected    not_detected   \n",
       "28    not_detected    not_detected         not_detected    not_detected   \n",
       "29    not_detected    not_detected         not_detected    not_detected   \n",
       "30    not_detected    not_detected         not_detected    not_detected   \n",
       "32    not_detected    not_detected         not_detected    not_detected   \n",
       "34    not_detected    not_detected         not_detected    not_detected   \n",
       "50    not_detected    not_detected         not_detected    not_detected   \n",
       "\n",
       "   Parainfluenza 2 Influenza B, rapid test Influenza A, rapid test  \n",
       "1     not_detected                negative                negative  \n",
       "8     not_detected                     NaN                     NaN  \n",
       "15    not_detected                negative                positive  \n",
       "18    not_detected                     NaN                     NaN  \n",
       "28    not_detected                     NaN                     NaN  \n",
       "29    not_detected                     NaN                     NaN  \n",
       "30    not_detected                negative                negative  \n",
       "32    not_detected                     NaN                     NaN  \n",
       "34    not_detected                     NaN                     NaN  \n",
       "50    not_detected                     NaN                     NaN  "
      ]
     },
     "execution_count": 210,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head(10)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Drop patient ID column and transform categorical variables into ordinal values"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 211,
   "metadata": {},
   "outputs": [],
   "source": [
    "df.drop(['Patient ID'], axis=1, inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 212,
   "metadata": {},
   "outputs": [],
   "source": [
    "def encode_categorical(df, categoricals): # TODO :- modify to ignore NaN\n",
    "    \"\"\" Encodes the categorical featurs\n",
    "    :param categorical_list: list of columns with not encoded categorical features\n",
    "    :type categorical_list: list(string)\n",
    "    \"\"\"\n",
    "    for category in categoricals:\n",
    "        df[category] = df[category].astype('category')\n",
    "        df[category] = df[category].cat.codes + 1\n",
    "    return df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 213,
   "metadata": {},
   "outputs": [],
   "source": [
    "categoricals = [\n",
    "    'SARS-Cov-2 exam result',\n",
    "    'Influenza A',\n",
    "    'Influenza B',\n",
    "    'Parainfluenza 1',\n",
    "    'CoronavirusNL63',\n",
    "    'Rhinovirus/Enterovirus',\n",
    "    'Coronavirus HKU1',\n",
    "    'Parainfluenza 3',\n",
    "    'Chlamydophila pneumoniae',\n",
    "    'Respiratory Syncytial Virus',\n",
    "    'Adenovirus',\n",
    "    'Parainfluenza 4',\n",
    "    'Coronavirus229E',\n",
    "    'CoronavirusOC43',\n",
    "    'Inf A H1N1 2009',\n",
    "    'Bordetella pertussis',\n",
    "    'Metapneumovirus',\n",
    "    'Parainfluenza 2',\n",
    "    'Influenza B, rapid test',\n",
    "    'Influenza A, rapid test',\n",
    "]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 214,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<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>Patient age quantile</th>\n",
       "      <th>SARS-Cov-2 exam result</th>\n",
       "      <th>Patient addmited to regular ward (1=yes, 0=no)</th>\n",
       "      <th>Patient addmited to semi-intensive unit (1=yes, 0=no)</th>\n",
       "      <th>Patient addmited to intensive care unit (1=yes, 0=no)</th>\n",
       "      <th>Hematocrit</th>\n",
       "      <th>Hemoglobin</th>\n",
       "      <th>Platelets</th>\n",
       "      <th>Red blood Cells</th>\n",
       "      <th>Lymphocytes</th>\n",
       "      <th>Mean corpuscular hemoglobin concentration (MCHC)</th>\n",
       "      <th>Leukocytes</th>\n",
       "      <th>Basophils</th>\n",
       "      <th>Mean corpuscular hemoglobin (MCH)</th>\n",
       "      <th>Eosinophils</th>\n",
       "      <th>Mean corpuscular volume (MCV)</th>\n",
       "      <th>Red blood cell distribution width (RDW)</th>\n",
       "      <th>Respiratory Syncytial Virus</th>\n",
       "      <th>Influenza A</th>\n",
       "      <th>Influenza B</th>\n",
       "      <th>Parainfluenza 1</th>\n",
       "      <th>CoronavirusNL63</th>\n",
       "      <th>Rhinovirus/Enterovirus</th>\n",
       "      <th>Coronavirus HKU1</th>\n",
       "      <th>Parainfluenza 3</th>\n",
       "      <th>Chlamydophila pneumoniae</th>\n",
       "      <th>Adenovirus</th>\n",
       "      <th>Parainfluenza 4</th>\n",
       "      <th>Coronavirus229E</th>\n",
       "      <th>CoronavirusOC43</th>\n",
       "      <th>Inf A H1N1 2009</th>\n",
       "      <th>Bordetella pertussis</th>\n",
       "      <th>Metapneumovirus</th>\n",
       "      <th>Parainfluenza 2</th>\n",
       "      <th>Influenza B, rapid test</th>\n",
       "      <th>Influenza A, rapid test</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>17</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.236515</td>\n",
       "      <td>-0.022340</td>\n",
       "      <td>-0.517413</td>\n",
       "      <td>0.102004</td>\n",
       "      <td>0.318366</td>\n",
       "      <td>-0.950790</td>\n",
       "      <td>-0.094610</td>\n",
       "      <td>-0.223767</td>\n",
       "      <td>-0.292269</td>\n",
       "      <td>1.482158</td>\n",
       "      <td>0.166192</td>\n",
       "      <td>-0.625073</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>-1.571682</td>\n",
       "      <td>-0.774212</td>\n",
       "      <td>1.429667</td>\n",
       "      <td>-0.850035</td>\n",
       "      <td>-0.005738</td>\n",
       "      <td>3.331071</td>\n",
       "      <td>0.364550</td>\n",
       "      <td>-0.223767</td>\n",
       "      <td>0.178175</td>\n",
       "      <td>1.018625</td>\n",
       "      <td>-1.336024</td>\n",
       "      <td>-0.978899</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>9</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>-0.747693</td>\n",
       "      <td>-0.586244</td>\n",
       "      <td>-0.429480</td>\n",
       "      <td>-1.361315</td>\n",
       "      <td>-1.114514</td>\n",
       "      <td>0.542882</td>\n",
       "      <td>-0.884923</td>\n",
       "      <td>0.081693</td>\n",
       "      <td>1.746323</td>\n",
       "      <td>-0.666950</td>\n",
       "      <td>1.668409</td>\n",
       "      <td>-1.067355</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>11</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0.991838</td>\n",
       "      <td>0.792188</td>\n",
       "      <td>0.072992</td>\n",
       "      <td>0.542763</td>\n",
       "      <td>0.045436</td>\n",
       "      <td>-0.452899</td>\n",
       "      <td>-0.211488</td>\n",
       "      <td>-0.834685</td>\n",
       "      <td>0.334989</td>\n",
       "      <td>-0.709090</td>\n",
       "      <td>0.606842</td>\n",
       "      <td>0.171035</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>13</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1.014726</td>\n",
       "      <td>0.854844</td>\n",
       "      <td>-0.178244</td>\n",
       "      <td>0.489872</td>\n",
       "      <td>-0.730707</td>\n",
       "      <td>-0.353319</td>\n",
       "      <td>-0.075131</td>\n",
       "      <td>2.525365</td>\n",
       "      <td>0.544077</td>\n",
       "      <td>0.217977</td>\n",
       "      <td>0.767079</td>\n",
       "      <td>0.171035</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    Patient age quantile  SARS-Cov-2 exam result  \\\n",
       "1                     17                       1   \n",
       "8                      1                       1   \n",
       "15                     9                       1   \n",
       "18                    11                       1   \n",
       "28                    13                       1   \n",
       "\n",
       "    Patient addmited to regular ward (1=yes, 0=no)  \\\n",
       "1                                                0   \n",
       "8                                                0   \n",
       "15                                               0   \n",
       "18                                               0   \n",
       "28                                               0   \n",
       "\n",
       "    Patient addmited to semi-intensive unit (1=yes, 0=no)  \\\n",
       "1                                                   0       \n",
       "8                                                   1       \n",
       "15                                                  0       \n",
       "18                                                  0       \n",
       "28                                                  0       \n",
       "\n",
       "    Patient addmited to intensive care unit (1=yes, 0=no)  Hematocrit  \\\n",
       "1                                                   0        0.236515   \n",
       "8                                                   0       -1.571682   \n",
       "15                                                  0       -0.747693   \n",
       "18                                                  0        0.991838   \n",
       "28                                                  0        1.014726   \n",
       "\n",
       "    Hemoglobin  Platelets  Red blood Cells  Lymphocytes  \\\n",
       "1    -0.022340  -0.517413         0.102004     0.318366   \n",
       "8    -0.774212   1.429667        -0.850035    -0.005738   \n",
       "15   -0.586244  -0.429480        -1.361315    -1.114514   \n",
       "18    0.792188   0.072992         0.542763     0.045436   \n",
       "28    0.854844  -0.178244         0.489872    -0.730707   \n",
       "\n",
       "    Mean corpuscular hemoglobin concentration (MCHC)  Leukocytes  Basophils  \\\n",
       "1                                          -0.950790   -0.094610  -0.223767   \n",
       "8                                           3.331071    0.364550  -0.223767   \n",
       "15                                          0.542882   -0.884923   0.081693   \n",
       "18                                         -0.452899   -0.211488  -0.834685   \n",
       "28                                         -0.353319   -0.075131   2.525365   \n",
       "\n",
       "    Mean corpuscular hemoglobin (MCH)  Eosinophils  \\\n",
       "1                           -0.292269     1.482158   \n",
       "8                            0.178175     1.018625   \n",
       "15                           1.746323    -0.666950   \n",
       "18                           0.334989    -0.709090   \n",
       "28                           0.544077     0.217977   \n",
       "\n",
       "    Mean corpuscular volume (MCV)  Red blood cell distribution width (RDW)  \\\n",
       "1                        0.166192                                -0.625073   \n",
       "8                       -1.336024                                -0.978899   \n",
       "15                       1.668409                                -1.067355   \n",
       "18                       0.606842                                 0.171035   \n",
       "28                       0.767079                                 0.171035   \n",
       "\n",
       "    Respiratory Syncytial Virus  Influenza A  Influenza B  Parainfluenza 1  \\\n",
       "1                             2            2            2                1   \n",
       "8                             2            2            2                1   \n",
       "15                            2            2            2                1   \n",
       "18                            2            2            2                1   \n",
       "28                            2            2            2                1   \n",
       "\n",
       "    CoronavirusNL63  Rhinovirus/Enterovirus  Coronavirus HKU1  \\\n",
       "1                 2                       1                 2   \n",
       "8                 2                       2                 2   \n",
       "15                2                       2                 2   \n",
       "18                2                       1                 2   \n",
       "28                2                       1                 2   \n",
       "\n",
       "    Parainfluenza 3  Chlamydophila pneumoniae  Adenovirus  Parainfluenza 4  \\\n",
       "1                 2                         1           2                2   \n",
       "8                 2                         1           2                2   \n",
       "15                2                         1           2                2   \n",
       "18                2                         1           2                2   \n",
       "28                2                         1           2                2   \n",
       "\n",
       "    Coronavirus229E  CoronavirusOC43  Inf A H1N1 2009  Bordetella pertussis  \\\n",
       "1                 2                2                2                     1   \n",
       "8                 2                2                2                     1   \n",
       "15                2                2                1                     1   \n",
       "18                2                2                2                     1   \n",
       "28                2                2                2                     1   \n",
       "\n",
       "    Metapneumovirus  Parainfluenza 2  Influenza B, rapid test  \\\n",
       "1                 2                1                        1   \n",
       "8                 2                1                        0   \n",
       "15                2                1                        1   \n",
       "18                2                1                        0   \n",
       "28                2                1                        0   \n",
       "\n",
       "    Influenza A, rapid test  \n",
       "1                         1  \n",
       "8                         0  \n",
       "15                        2  \n",
       "18                        0  \n",
       "28                        0  "
      ]
     },
     "execution_count": 214,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df = encode_categorical(df, categoricals)\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Fill missing value of each column with column average value "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 215,
   "metadata": {},
   "outputs": [],
   "source": [
    "for column in df.columns:\n",
    "    df[column].fillna(df[column].mean(), inplace=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 217,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 217,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.isna().sum().sum() == 0"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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