DSA_SS24/notebooks/statistics.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Hypothesis\n",
    "This notebook is used to read the data from the pickle files and to test the hypothesis that in the age group of 60-70 the frequency of a sinus bradycardia is significantly higher than in the other age groups.\n",
    "For that instance the chi-squared test is used."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import seaborn as sns\n",
    "import matplotlib.pyplot as plt\n",
    "import pickle\n",
    "import sys\n",
    "\n",
    "\n",
    "from scipy.stats import chi2_contingency\n",
    "sys.path.append('../scripts')\n",
    "import data_helper\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading GSVT\n",
      "Reading AFIB\n",
      "Reading SR\n",
      "Reading SB\n",
      "Number of patients per category:\n",
      "GSVT: 0\n",
      "AFIB: 27\n",
      "SR: 13\n",
      "SB: 50\n"
     ]
    }
   ],
   "source": [
    "data = data_helper.load_data(only_demographic=False)\n",
    "\n",
    "print(\"Number of patients per category:\")\n",
    "for cat_name in data.keys():\n",
    "    print(f\"{cat_name}: {len(data[cat_name])}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Reading GSVT\n",
      "Reading AFIB\n",
      "Reading SR\n",
      "Reading SB\n"
     ]
    },
    {
     "ename": "ValueError",
     "evalue": "All arrays must be of the same length",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mValueError\u001b[0m                                Traceback (most recent call last)",
      "Cell \u001b[1;32mIn[27], line 3\u001b[0m\n\u001b[0;32m      1\u001b[0m data_org \u001b[38;5;241m=\u001b[39m data_helper\u001b[38;5;241m.\u001b[39mload_data(only_demographic\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m)\n\u001b[1;32m----> 3\u001b[0m df_dgc \u001b[38;5;241m=\u001b[39m \u001b[43mpd\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mDataFrame\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdata_org\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[1;32m~\\AppData\\Local\\Packages\\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\\LocalCache\\local-packages\\Python311\\site-packages\\pandas\\core\\frame.py:767\u001b[0m, in \u001b[0;36mDataFrame.__init__\u001b[1;34m(self, data, index, columns, dtype, copy)\u001b[0m\n\u001b[0;32m    761\u001b[0m     mgr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_init_mgr(\n\u001b[0;32m    762\u001b[0m         data, axes\u001b[38;5;241m=\u001b[39m{\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mindex\u001b[39m\u001b[38;5;124m\"\u001b[39m: index, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mcolumns\u001b[39m\u001b[38;5;124m\"\u001b[39m: columns}, dtype\u001b[38;5;241m=\u001b[39mdtype, copy\u001b[38;5;241m=\u001b[39mcopy\n\u001b[0;32m    763\u001b[0m     )\n\u001b[0;32m    765\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(data, \u001b[38;5;28mdict\u001b[39m):\n\u001b[0;32m    766\u001b[0m     \u001b[38;5;66;03m# GH#38939 de facto copy defaults to False only in non-dict cases\u001b[39;00m\n\u001b[1;32m--> 767\u001b[0m     mgr \u001b[38;5;241m=\u001b[39m \u001b[43mdict_to_mgr\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdata\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcolumns\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdtype\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcopy\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcopy\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtyp\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mmanager\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m    768\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(data, ma\u001b[38;5;241m.\u001b[39mMaskedArray):\n\u001b[0;32m    769\u001b[0m     \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mnumpy\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mma\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m mrecords\n",
      "File \u001b[1;32m~\\AppData\\Local\\Packages\\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\\LocalCache\\local-packages\\Python311\\site-packages\\pandas\\core\\internals\\construction.py:503\u001b[0m, in \u001b[0;36mdict_to_mgr\u001b[1;34m(data, index, columns, dtype, typ, copy)\u001b[0m\n\u001b[0;32m    499\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m    500\u001b[0m         \u001b[38;5;66;03m# dtype check to exclude e.g. range objects, scalars\u001b[39;00m\n\u001b[0;32m    501\u001b[0m         arrays \u001b[38;5;241m=\u001b[39m [x\u001b[38;5;241m.\u001b[39mcopy() \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mhasattr\u001b[39m(x, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m) \u001b[38;5;28;01melse\u001b[39;00m x \u001b[38;5;28;01mfor\u001b[39;00m x \u001b[38;5;129;01min\u001b[39;00m arrays]\n\u001b[1;32m--> 503\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43marrays_to_mgr\u001b[49m\u001b[43m(\u001b[49m\u001b[43marrays\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mcolumns\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindex\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mdtype\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdtype\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mtyp\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtyp\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mconsolidate\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mcopy\u001b[49m\u001b[43m)\u001b[49m\n",
      "File \u001b[1;32m~\\AppData\\Local\\Packages\\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\\LocalCache\\local-packages\\Python311\\site-packages\\pandas\\core\\internals\\construction.py:114\u001b[0m, in \u001b[0;36marrays_to_mgr\u001b[1;34m(arrays, columns, index, dtype, verify_integrity, typ, consolidate)\u001b[0m\n\u001b[0;32m    111\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m verify_integrity:\n\u001b[0;32m    112\u001b[0m     \u001b[38;5;66;03m# figure out the index, if necessary\u001b[39;00m\n\u001b[0;32m    113\u001b[0m     \u001b[38;5;28;01mif\u001b[39;00m index \u001b[38;5;129;01mis\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m--> 114\u001b[0m         index \u001b[38;5;241m=\u001b[39m \u001b[43m_extract_index\u001b[49m\u001b[43m(\u001b[49m\u001b[43marrays\u001b[49m\u001b[43m)\u001b[49m\n\u001b[0;32m    115\u001b[0m     \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m    116\u001b[0m         index \u001b[38;5;241m=\u001b[39m ensure_index(index)\n",
      "File \u001b[1;32m~\\AppData\\Local\\Packages\\PythonSoftwareFoundation.Python.3.11_qbz5n2kfra8p0\\LocalCache\\local-packages\\Python311\\site-packages\\pandas\\core\\internals\\construction.py:677\u001b[0m, in \u001b[0;36m_extract_index\u001b[1;34m(data)\u001b[0m\n\u001b[0;32m    675\u001b[0m lengths \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(\u001b[38;5;28mset\u001b[39m(raw_lengths))\n\u001b[0;32m    676\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(lengths) \u001b[38;5;241m>\u001b[39m \u001b[38;5;241m1\u001b[39m:\n\u001b[1;32m--> 677\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAll arrays must be of the same length\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[0;32m    679\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m have_dicts:\n\u001b[0;32m    680\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mValueError\u001b[39;00m(\n\u001b[0;32m    681\u001b[0m         \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mMixing dicts with non-Series may lead to ambiguous ordering.\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m    682\u001b[0m     )\n",
      "\u001b[1;31mValueError\u001b[0m: All arrays must be of the same length"
     ]
    }
   ],
   "source": [
    "data_org = data_helper.load_data(only_demographic=False)\n",
    "\n",
    "df_dgc = pd.DataFrame(data_org)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "ename": "NameError",
     "evalue": "name 'df_dgc' is not defined",
     "output_type": "error",
     "traceback": [
      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
      "Cell \u001b[1;32mIn[21], line 36\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;66;03m# #path = \"C:/Studium/dsa/data\"\u001b[39;00m\n\u001b[0;32m      2\u001b[0m \u001b[38;5;66;03m# #path = \"C:/Users/Nils/Documents/HS-Mannheim/0000_MASTER/DSA/EKG_Prog/data\"\u001b[39;00m\n\u001b[0;32m      3\u001b[0m \u001b[38;5;66;03m# path = \"C:/Users/klara/projects/DSA/data\"\u001b[39;00m\n\u001b[1;32m   (...)\u001b[0m\n\u001b[0;32m     33\u001b[0m \n\u001b[0;32m     34\u001b[0m \u001b[38;5;66;03m# Change from group to category\u001b[39;00m\n\u001b[0;32m     35\u001b[0m age_categories \u001b[38;5;241m=\u001b[39m [\u001b[38;5;241m0\u001b[39m, \u001b[38;5;241m10\u001b[39m, \u001b[38;5;241m20\u001b[39m, \u001b[38;5;241m30\u001b[39m, \u001b[38;5;241m40\u001b[39m, \u001b[38;5;241m50\u001b[39m, \u001b[38;5;241m60\u001b[39m, \u001b[38;5;241m70\u001b[39m, \u001b[38;5;241m80\u001b[39m, \u001b[38;5;241m90\u001b[39m]\n\u001b[1;32m---> 36\u001b[0m df_dgc[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mage_group\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mcut(\u001b[43mdf_dgc\u001b[49m[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mage\u001b[39m\u001b[38;5;124m'\u001b[39m], bins\u001b[38;5;241m=\u001b[39mage_categories)\n\u001b[0;32m     37\u001b[0m corr_matrix_age_diag\u001b[38;5;241m=\u001b[39m pd\u001b[38;5;241m.\u001b[39mcrosstab(df_dgc[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mage_group\u001b[39m\u001b[38;5;124m'\u001b[39m], df_dgc[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdiag\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[0;32m     39\u001b[0m \u001b[38;5;66;03m# Chi-square test\u001b[39;00m\n",
      "\u001b[1;31mNameError\u001b[0m: name 'df_dgc' is not defined"
     ]
    }
   ],
   "source": [
    "# #path = \"C:/Studium/dsa/data\"\n",
    "# #path = \"C:/Users/Nils/Documents/HS-Mannheim/0000_MASTER/DSA/EKG_Prog/data\"\n",
    "# path = \"C:/Users/klara/projects/DSA/data\"\n",
    "\n",
    "# categories_dict = {\n",
    "# 'SB':    [426177001],\n",
    "# 'AFIB':  [164889003, 164890007],\n",
    "# 'GSVT':  [426761007, 713422000, 233896004, 233897008, 713422000],\n",
    "# 'SR':    [426783006, 427393009]\n",
    "# }\n",
    "\n",
    "# data = {}\n",
    "# for cat_name in categories_dict.keys():\n",
    "#     print(f\"Reading {cat_name}\")\n",
    "#     with open(f'{path}/{cat_name}.pkl', 'rb') as f:\n",
    "#         records = pickle.load(f)\n",
    "#         data[cat_name] = records\n",
    "#         print(f\"Length of {cat_name}: {len(records)}\")\n",
    "\n",
    "# data_demographic = {'age':[], 'diag':[], 'gender':[]}\n",
    "# for cat_name, records in data.items():\n",
    "#     for record in records:\n",
    "#         age = record.comments[0].split(' ')[1]\n",
    "#         sex = record.comments[1].split(' ')[1]\n",
    "#         if age == 'NaN' or sex == 'NaN':\n",
    "#             continue\n",
    "#         # cut Age: from alter string \n",
    "#         data_demographic['age'].append(int(age))\n",
    "#         data_demographic['diag'].append(cat_name)\n",
    "#         data_demographic['gender'].append(sex)\n",
    "\n",
    "# df_dgc = pd.DataFrame(data_demographic)\n",
    "\n",
    "# Change from group to category\n",
    "age_categories = [0, 10, 20, 30, 40, 50, 60, 70, 80, 90]\n",
    "df_dgc['age_group'] = pd.cut(df_dgc['age'], bins=age_categories)\n",
    "corr_matrix_age_diag= pd.crosstab(df_dgc['age_group'], df_dgc['diag'])\n",
    "\n",
    "# Chi-square test\n",
    "chi2, p, _, _ = chi2_contingency(corr_matrix_age_diag)\n",
    "\n",
    "# Difference between observed and expected frequencies\n",
    "print(f\"Chi-Square Statistic: {chi2}\")\n",
    "print(f\"P-value: {p}\")\n",
    "\n",
    "# Check if SB (Sinusbradykardie) has a significantly higher frequency in the 60-70 age group\n",
    "sb_60_70 = corr_matrix_age_diag.loc[pd.Interval(60, 70, closed='right'), 'SB']\n",
    "sb_other = corr_matrix_age_diag.drop(pd.Interval(60, 70, closed='right')).sum()['SB']\n",
    "total_60_70 = corr_matrix_age_diag.loc[pd.Interval(60, 70, closed='right')].sum()\n",
    "total_other = corr_matrix_age_diag.drop(pd.Interval(60, 70, closed='right')).sum().sum()\n",
    "\n",
    "# Frequency table for the specific Chi-Square test\n",
    "observed = [[sb_60_70, total_60_70 - sb_60_70], [sb_other, total_other - sb_other]]\n",
    "chi2_sb, p_sb = chi2_contingency(observed)[:2]\n",
    "\n",
    "\n",
    "print(f\"Chi-Square Statistic for SB in 60-70 vs others: {chi2_sb}\")\n",
    "print(f\"P-value for SB in 60-70 vs others: {p_sb}\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The results can be interpreted as followed:\n",
    "\n",
    "- The first value returned is the Chi-Square Statistic that shows the difference between the observed and the expected frequencies. Here, a bigger number indicates a bigger difference. The p-value shows the probability of this difference being statistically significant. If the p-value is below the significance level of 0.05, the difference is significant.\n",
    "\n",
    "- The Chi-Square Statistic for sinus bradycardia in the age group 60-70 compared to the other age groups, is a value that shows whether there is a significant difference in the frequency of sinus bradycardia in the age group 60-70 in comparison to the other age groups. If the p-value is smaller than the significance level of 0.05, the difference in the frequency between the age group 60-70 and the other age groups is significant."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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