risk.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true,
    "scrolled": false
   },
   "outputs": [],
   "source": [
    "from enum import Enum,IntEnum\n",
    "from functools import reduce\n",
    "from datetime import datetime\n",
    "from pyDatalog import pyDatalog\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def load_facts():\n",
    "  \n",
    "  load_cc_facts(\"icd10.txt\",0)\n",
    "  load_cc_facts(\"icd9.txt\",9)\n",
    "  load_hcc_facts()\n",
    "  load_diagnostic_category_facts()\n",
    "  load_coefficients(\"coefficients.txt\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "global vals\n",
    "def load_coefficients(f):\n",
    "    dir = os.path.dirname(os.path.abspath(\"__file__\"))\n",
    "    file = open(os.path.join(dir,\"coefficients.txt\"), 'r')                                     \n",
    "    for line in file:\n",
    "        vals = map(lambda s: s.strip(),line.split(\",\"))\n",
    "        print(vals)\n",
    "#         print(vals)\n",
    "#         label,coeff = vals\n",
    "#         print(label,float(coeff))\n",
    "#     + coefficient(label,float(coeff)) \n",
    "#   + coefficient('starting',0.00)\n",
    "# print(label,float(coeff))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def load_cc_facts(f,icdcodetype):\n",
    "  dir = os.path.dirname(os.path.abspath(\"__file__\"))\n",
    "  file = open(os.path.join(dir,\"icd10.txt\"), 'r')                                     \n",
    "  for line in file:\n",
    "    vals = line.split()\n",
    "    vals\n",
    "#     if len(vals) == 2:\n",
    "#       icdE,ccE = vals\n",
    "#     elif len(vals) == 3:\n",
    "#       icdE,ccE,_ = vals\n",
    "#     + cc(icdE,ccE,icdcodetype) \n",
    "\n",
    "def load_hcc_facts():\n",
    "  overriders = [\n",
    "          (\"8\",[\"9\",\"10\",\"11\",\"12\" ]),\n",
    "          (\"9\",[\"10\",\"11\",\"12\" ]),\n",
    "          (\"10\",[\"11\",\"12\" ]),\n",
    "          (\"11\",[\"12\" ]),\n",
    "          (\"17\",[\"18\",\"19\" ]),\n",
    "          (\"18\",[\"19\" ]),\n",
    "          (\"27\",[\"28\",\"29\",\"80\" ]),\n",
    "          (\"28\",[\"29\" ]),\n",
    "          (\"46\",[\"48\" ]),\n",
    "          (\"51\",[\"52\" ]),\n",
    "          (\"54\",[\"55\" ]),\n",
    "          (\"57\",[\"58\" ]),\n",
    "          (\"70\",[\"71\",\"72\",\"103\",\"104\",\"169\" ]),\n",
    "          (\"71\",[\"72\",\"104\",\"169\" ]),\n",
    "          (\"72\",[\"169\" ]),\n",
    "          (\"82\",[\"83\",\"84\" ]),\n",
    "          (\"83\",[\"84\" ]),\n",
    "          (\"86\",[\"87\",\"88\" ]),\n",
    "          (\"87\",[\"88\" ]),\n",
    "          (\"99\",[\"100\" ]),\n",
    "          (\"103\",[\"104\" ]),\n",
    "          (\"106\",[\"107\",\"108\",\"161\",\"189\" ]),\n",
    "          (\"107\",[\"108\" ]),\n",
    "          (\"110\",[\"111\",\"112\" ]),\n",
    "          (\"111\",[\"112\" ]),\n",
    "          (\"114\",[\"115\" ]),\n",
    "          (\"134\",[\"135\",\"136\",\"137\",\"138\",\"139\",\"140\",\"141\"]),\n",
    "          (\"135\",[\"136\",\"137\",\"138\",\"139\",\"140\",\"141\" ]),\n",
    "          (\"136\",[\"137\",\"138\",\"139\",\"140\",\"141\" ]),\n",
    "          (\"137\",[\"138\",\"139\",\"140\",\"141\" ]),\n",
    "          (\"138\",[\"139\",\"140\",\"141\" ]),\n",
    "          (\"139\",[\"140\",\"141\" ]),\n",
    "          (\"140\",[\"141\" ]),\n",
    "          (\"157\",[\"158\",\"159\",\"160\",\"161\" ]),\n",
    "          (\"158\",[\"159\",\"160\",\"161\" ]),\n",
    "          (\"159\",[\"160\",\"161\" ]),\n",
    "          (\"160\",[\"161\" ]),\n",
    "          (\"166\",[\"80\",\"167\" ])\n",
    "          ]\n",
    "#   for overrider, overridees in overriders:\n",
    "#     for overridee in overridees:\n",
    "#       + overrides(overrider,overridee)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from hcc import *\n",
    "cvars= community_regression()\n",
    "####################################################\n",
    "jane = Beneficiary(2,\"female\",\"19740824\",EntitlementReason.DIB,True)\n",
    "jane.add_diagnosis(Diagnosis(jane,\"D66\",ICDType.TEN))  \n",
    "jane.add_diagnosis(Diagnosis(jane,\"C182\",ICDType.TEN))  \n",
    "\n",
    "daniel = Beneficiary(1,\"male\",\"19740824\",EntitlementReason.DIB)\n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"A0223\",ICDType.TEN))  # 51\n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"A0224\",ICDType.TEN))  # 52\n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"D66\",ICDType.TEN))  \n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"C163\",ICDType.TEN))  \n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"C163\",ICDType.TEN))  \n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"C182\",ICDType.TEN))  \n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"C800\",ICDType.TEN))  \n",
    "daniel.add_diagnosis(Diagnosis(daniel,\"A072\",ICDType.TEN))  \n",
    "\n",
    "bob = Beneficiary(3,\"male\",\"20040824\",EntitlementReason.DIB,True)\n",
    "bob.add_diagnosis(Diagnosis(bob,\"A0223\",ICDType.TEN))\n",
    "bob.add_diagnosis(Diagnosis(bob,\"A0224\",ICDType.TEN))\n",
    "\n",
    "jacob = Beneficiary(4,\"male\",\"1940824\",EntitlementReason.DIB,True)\n",
    "\n",
    "antonio = Beneficiary(3,\"male\",\"20040824\",EntitlementReason.DIB,True)\n",
    "antonio.add_diagnosis(Diagnosis(antonio,\"A0223\",ICDType.TEN))\n",
    "antonio.add_diagnosis(Diagnosis(antonio,\"49320\",ICDType.NINE))\n",
    "\n",
    "john = Beneficiary(5,\"male\",\"19920824\",EntitlementReason.DIB,True)\n",
    "john.add_diagnosis(Diagnosis(john,\"A0223\",ICDType.TEN))\n",
    "john.add_diagnosis(Diagnosis(john,\"49320\",ICDType.NINE))\n",
    "\n",
    "####################################################"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[ID:5,DOB:1992-08-24 00:00:00A0223ICDType.TEN,\n",
       " ID:5,DOB:1992-08-24 00:00:0049320ICDType.NINE]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "john = Beneficiary(5,\"male\",\"19920824\",EntitlementReason.DIB,True)\n",
    "john.add_diagnosis(Diagnosis(john,\"A0223\",ICDType.TEN))\n",
    "john.add_diagnosis(Diagnosis(john,\"49320\",ICDType.NINE))\n",
    "john.diagnoses"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "jane = Beneficiary(hicno='0220F11E0B2EC004', sex='female', dob='19480601')\n",
    "jane_alt = Beneficiary(hicno='0220F11E0B2EC004', sex='male', dob='19480601')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'female'"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "jane_sex = Beneficiary(hicno='0220F11E0B2EC004', sex='female', dob='19480601').sex\n",
    "Ben=Beneficiary\n",
    "jane_sex"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 48,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>HICNO</th>\n",
       "      <th>SEX</th>\n",
       "      <th>DOB</th>\n",
       "      <th>MCAID</th>\n",
       "      <th>NEMCAID</th>\n",
       "      <th>OREC</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6348</td>\n",
       "      <td>1</td>\n",
       "      <td>1952-12-19</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>75644</td>\n",
       "      <td>1</td>\n",
       "      <td>1956-05-16</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>97652</td>\n",
       "      <td>1</td>\n",
       "      <td>1948-06-30</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>345678</td>\n",
       "      <td>2</td>\n",
       "      <td>1956-12-07</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>553553</td>\n",
       "      <td>2</td>\n",
       "      <td>1964-01-13</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>564416</td>\n",
       "      <td>2</td>\n",
       "      <td>1948-01-10</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>576542</td>\n",
       "      <td>1</td>\n",
       "      <td>1956-02-26</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>1515655</td>\n",
       "      <td>2</td>\n",
       "      <td>1959-06-23</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>3737486</td>\n",
       "      <td>2</td>\n",
       "      <td>1950-02-18</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>5444646</td>\n",
       "      <td>2</td>\n",
       "      <td>1946-02-02</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>5453646</td>\n",
       "      <td>1</td>\n",
       "      <td>1954-06-20</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "      HICNO  SEX        DOB  MCAID  NEMCAID  OREC\n",
       "0      6348    1 1952-12-19      1        1     4\n",
       "1     75644    1 1956-05-16      1        0     3\n",
       "2     97652    1 1948-06-30      1        1     1\n",
       "3    345678    2 1956-12-07      1        1     3\n",
       "4    553553    2 1964-01-13      0        0     2\n",
       "5    564416    2 1948-01-10      1        0     1\n",
       "6    576542    1 1956-02-26      0        1     2\n",
       "7   1515655    2 1959-06-23      0        0     4\n",
       "8   3737486    2 1950-02-18      1        1     3\n",
       "9   5444646    2 1946-02-02      0        0     1\n",
       "10  5453646    1 1954-06-20      0        0     1"
      ]
     },
     "execution_count": 48,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "Person=pd.read_excel(\"Person.xlsx\",sheetname='Person',convertors={'SEX':str ,'OREC': str})\n",
    "Diag=pd.read_excel(\"Person.xlsx\",sheetname='Diag',convertors={'Diagnosis': str})\n",
    "\n",
    "Person.sort_values(['HICNO'],inplace=True)\n",
    "Diag.sort_values(['HICNO'],inplace=True)\n",
    "\n",
    "\n",
    "cohort_study=pd.merge(Person[['HICNO','SEX','DOB']], Diag, how='inner', on='HICNO')\n",
    "cohort_study.groupby(['HICNO','SEX','DOB']).count().reset_index().sort_values('Diagnosis',ascending=False)['Diagnosis']>0\n",
    "cohort_study1=cohort_study[cohort_study.groupby(['HICNO','SEX','DOB']).count().reset_index().sort_values\\\n",
    "('Diagnosis',ascending=False)['Diagnosis']>0][['HICNO','SEX','DOB']]\n",
    "\n",
    "# Adding medicaid,nemcaid\n",
    "cohort_study2=pd.merge(cohort_study[['HICNO','SEX','DOB']], Person[['HICNO','MCAID','NEMCAID','OREC']], how='inner', on='HICNO')\n",
    "# cohort_study = %sql \\\n",
    "#     SELECT d.PatientID, p.SEX, p.DOB \\\n",
    "#         from diagnoses d join mem.patients p\\\n",
    "#                 on d.PatientID = p.PATIENT_ID\\\n",
    "#         group by PatientID,p.SEX, p.DOB\\\n",
    "#         having COUNT(*) > 20\\\n",
    "#         order by Count(*) desc\\\n",
    "#         limit 100;\n",
    "cohort_study2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 64,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def gender(l):\n",
    "    if l == 'M':\n",
    "        return 'male'\n",
    "    else:\n",
    "        return 'female'\n",
    "\n",
    "\n",
    "cohort_patients = [Beneficiary(hicno=row[0], sex=gender(row[1]), dob=str(row[2].date()).replace(\"-\",\"\"),\\\n",
    "                               medicaid=bool(row[3]),newenrollee_medicaid=bool(row[4]),original_reason_entitlement=row[5]) for index,row in cohort_study2.iterrows()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 55,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "hicno = [pat.hicno for pat in cohort_patients]\n",
    "hicno = tuple(hicno)\n",
    "diags=Diag[Diag['HICNO']==hicno]\n",
    "diags.head()\n",
    "# diags = %sql SELECT DISTINCT PatientID, Diagnosis from diagnoses where PatientID in $hicno\n",
    "diags = diags.set_index('HICNO')\n",
    "\n",
    "for pat in cohort_patients:\n",
    "    pat_diags = diags['Diagnosis'].loc[pat.hicno]\n",
    "    pat.add_diagnosis(Diagnosis(pat,pat_diags,ICDType.TEN))\n",
    "#     print(pat.diagnoses)\n",
    "#     for code in pat_diags:\n",
    "#         pat.add_diagnosis(Diagnosis(pat,code,ICDType.NINE))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {
    "collapsed": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "F0_34 0 []\n",
      "F35_44 1 [(ID:2,DOB:1974-08-24 00:00:00,)]\n",
      "F45_54 1 [(ID:553553,DOB:1964-01-13 00:00:00,), (ID:553553,DOB:1964-01-13 00:00:00,)]\n",
      "F55_59 1 [(ID:1515655,DOB:1959-06-23 00:00:00,), (ID:1515655,DOB:1959-06-23 00:00:00,)]\n",
      "F60_64 1 [(ID:75644,DOB:1956-05-16 00:00:00,), (ID:576542,DOB:1956-02-26 00:00:00,), (ID:345678,DOB:1956-12-07 00:00:00,), (ID:576542,DOB:1956-02-26 00:00:00,), (ID:345678,DOB:1956-12-07 00:00:00,), (ID:5453646,DOB:1954-06-20 00:00:00,), (ID:75644,DOB:1956-05-16 00:00:00,), (ID:5453646,DOB:1954-06-20 00:00:00,)]\n",
      "F65_69 1 [(ID:0220F11E0B2EC004,DOB:1948-06-01 00:00:00,), (ID:97652,DOB:1948-06-30 00:00:00,), (ID:97652,DOB:1948-06-30 00:00:00,), (ID:3737486,DOB:1950-02-18 00:00:00,), (ID:3737486,DOB:1950-02-18 00:00:00,)]\n",
      "F70_74 1 [(ID:5444646,DOB:1946-02-02 00:00:00,), (ID:5444646,DOB:1946-02-02 00:00:00,)]\n",
      "F75_79 0 []\n",
      "F80_84 0 []\n",
      "F85_89 0 []\n",
      "F90_94 0 []\n",
      "F95_GT 0 []\n",
      "M0_34 1 [(ID:3,DOB:2004-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,)]\n",
      "M35_44 1 [(ID:1,DOB:1974-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,)]\n",
      "M45_54 0 []\n",
      "M55_59 0 []\n",
      "M60_64 0 []\n",
      "M65_69 1 [(ID:0220F11E0B2EC004,DOB:1948-06-01 00:00:00,)]\n",
      "M70_74 0 []\n",
      "M75_79 1 [(ID:4,DOB:1940-08-24 00:00:00,), (ID:4,DOB:1940-08-24 00:00:00,)]\n",
      "M80_84 0 []\n",
      "M85_89 0 []\n",
      "M90_94 0 []\n",
      "M95_GT 0 []\n",
      "MCAID_Female_Aged 1 [(ID:6348,DOB:1952-12-19 00:00:00,), (ID:97652,DOB:1948-06-30 00:00:00,), (ID:97652,DOB:1948-06-30 00:00:00,), (ID:564416,DOB:1948-01-10 00:00:00,), (ID:3737486,DOB:1950-02-18 00:00:00,), (ID:6348,DOB:1952-12-19 00:00:00,), (ID:564416,DOB:1948-01-10 00:00:00,), (ID:3737486,DOB:1950-02-18 00:00:00,)]\n",
      "MCAID_Female_Disabled 1 [(ID:3,DOB:2004-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,)]\n",
      "MCAID_Male_Aged 1 [(ID:4,DOB:1940-08-24 00:00:00,), (ID:4,DOB:1940-08-24 00:00:00,)]\n",
      "MCAID_Male_Disabled 1 [(ID:3,DOB:2004-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,)]\n",
      "OriginallyDisabled_Female 1 [(ID:5444646,DOB:1946-02-02 00:00:00,), (ID:97652,DOB:1948-06-30 00:00:00,), (ID:97652,DOB:1948-06-30 00:00:00,), (ID:564416,DOB:1948-01-10 00:00:00,), (ID:5444646,DOB:1946-02-02 00:00:00,), (ID:564416,DOB:1948-01-10 00:00:00,)]\n",
      "OriginallyDisabled_Male 1 [(ID:4,DOB:1940-08-24 00:00:00,), (ID:4,DOB:1940-08-24 00:00:00,)]\n",
      "DISABLED_HCC6 1 [(ID:1,DOB:1974-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,)]\n",
      "DISABLED_HCC34 0 []\n",
      "DISABLED_HCC46 1 [(ID:1,DOB:1974-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,)]\n",
      "DISABLED_HCC54 0 []\n",
      "DISABLED_HCC55 0 []\n",
      "DISABLED_HCC110 0 []\n",
      "DISABLED_HCC176 0 []\n",
      "SEPSIS_CARD_RESP_FAIL 0 []\n",
      "CANCER_IMMUNE 0 []\n",
      "DIABETES_CHF 0 []\n",
      "CHF_COPD 0 []\n",
      "CHF_RENAL 0 []\n",
      "COPD_CARD_RESP_FAIL 0 []\n",
      "HCC1 1 [(ID:1515655,DOB:1959-06-23 00:00:00,)]\n",
      "HCC2 0 []\n",
      "HCC6 1 [(ID:1,DOB:1974-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,)]\n",
      "HCC8 1 [(ID:1,DOB:1974-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,)]\n",
      "HCC9 0 []\n",
      "HCC10 0 []\n",
      "HCC11 1 [(ID:2,DOB:1974-08-24 00:00:00,)]\n",
      "HCC12 0 []\n",
      "HCC17 0 []\n",
      "HCC18 0 []\n",
      "HCC19 0 []\n",
      "HCC21 0 []\n",
      "HCC22 0 []\n",
      "HCC23 0 []\n",
      "HCC27 0 []\n",
      "HCC28 0 []\n",
      "HCC29 0 []\n",
      "HCC33 0 []\n",
      "HCC34 0 []\n",
      "HCC35 0 []\n",
      "HCC39 1 [(ID:5,DOB:1992-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:3,DOB:2004-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,)]\n",
      "HCC40 0 []\n",
      "HCC46 1 [(ID:1,DOB:1974-08-24 00:00:00,), (ID:1,DOB:1974-08-24 00:00:00,)]\n",
      "HCC47 0 []\n",
      "HCC48 1 [(ID:2,DOB:1974-08-24 00:00:00,)]\n",
      "HCC51 0 []\n",
      "HCC52 0 []\n",
      "HCC54 0 []\n",
      "HCC55 0 []\n",
      "HCC57 0 []\n",
      "HCC58 0 []\n",
      "HCC70 0 []\n",
      "HCC71 0 []\n",
      "HCC72 0 []\n",
      "HCC73 0 []\n",
      "HCC74 0 []\n",
      "HCC75 0 []\n",
      "HCC76 0 []\n",
      "HCC77 0 []\n",
      "HCC78 0 []\n",
      "HCC79 0 []\n",
      "HCC80 0 []\n",
      "HCC82 0 []\n",
      "HCC83 0 []\n",
      "HCC84 0 []\n",
      "HCC85 0 []\n",
      "HCC86 0 []\n",
      "HCC87 0 []\n",
      "HCC88 0 []\n",
      "HCC96 0 []\n",
      "HCC99 0 []\n",
      "HCC100 0 []\n",
      "HCC103 0 []\n",
      "HCC104 0 []\n",
      "HCC106 0 []\n",
      "HCC107 0 []\n",
      "HCC108 0 []\n",
      "HCC110 0 []\n",
      "HCC111 1 [(ID:5,DOB:1992-08-24 00:00:00,), (ID:5,DOB:1992-08-24 00:00:00,)]\n",
      "HCC112 0 []\n",
      "HCC114 0 []\n",
      "HCC115 0 []\n",
      "HCC122 0 []\n",
      "HCC124 0 []\n",
      "HCC134 0 []\n",
      "HCC135 0 []\n",
      "HCC136 0 []\n",
      "HCC137 0 []\n",
      "HCC138 0 []\n",
      "HCC139 0 []\n",
      "HCC140 0 []\n",
      "HCC141 0 []\n",
      "HCC157 0 []\n",
      "HCC158 0 []\n",
      "HCC159 0 []\n",
      "HCC160 0 []\n",
      "HCC161 0 []\n",
      "HCC162 0 []\n",
      "HCC166 0 []\n",
      "HCC167 0 []\n",
      "HCC169 0 []\n",
      "HCC170 0 []\n",
      "HCC173 0 []\n",
      "HCC176 0 []\n",
      "HCC186 0 []\n",
      "HCC188 0 []\n",
      "HCC189 0 []\n"
     ]
    }
   ],
   "source": [
    "def dummy(a):\n",
    "    if a == '[]':\n",
    "        b=0\n",
    "    else:\n",
    "        b=1\n",
    "    return b\n",
    "\n",
    "for CC in cvars:\n",
    "    print(CC, dummy(str(indicator(B,CC).data)),indicator(B,CC).data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 66,
   "metadata": {
    "collapsed": true,
    "scrolled": true
   },
   "outputs": [],
   "source": [
    "patients=pd.DataFrame()\n",
    "patients1=[]\n",
    "sex1=[]\n",
    "dob1=[]\n",
    "medicaid1=[]\n",
    "nemcaid1=[]\n",
    "orec1=[]\n",
    "# diagnoses1=[]\n",
    "\n",
    "for pat in cohort_patients:\n",
    "    patients1.append((str(pat.hicno)))\n",
    "    sex1.append((str(pat.sex)))\n",
    "    dob1.append((str(pat.dob)))\n",
    "    medicaid1.append((str(pat.medicaid)))\n",
    "    nemcaid1.append((str(pat.newenrollee_medicaid)))\n",
    "    orec1.append((str(pat.original_reason_entitlement)))\n",
    "#     diagnoses1.append((str(pat.diagnoses)))\n",
    "#     for CC in cvars:\n",
    "#         print(CC, dummy(str(indicator(pat,CC).data)))\n",
    "patients['hicno']=patients1\n",
    "patients['sex']=sex1\n",
    "patients['DOB']=dob1\n",
    "patients['MCAID']=medicaid1\n",
    "patients['NEMCAID']=nemcaid1\n",
    "\n",
    "# patients['diagnoses']=diagnoses1\n",
    "\n",
    "for CC in cvars:\n",
    "    CC1=[]\n",
    "    CC2=[] # just for checking, remove afterwards\n",
    "    for pat in cohort_patients:\n",
    "        CC1.append(dummy(str(indicator(pat,CC).data)))\n",
    "        CC2.append(str(indicator(pat,CC).data)) # just for checking, remove afterwards\n",
    "#         print(CC, dummy(str(indicator(pat,CC).data)))\n",
    "    patients[CC]=CC1\n",
    "    patients[CC+'_data']=CC2 # just for checking, remove afterwards\n",
    "# patients.set_index('hicno')\n",
    "\n",
    "# for pat in patients:\n",
    "#     patients['sex'] = cohort_study['SEX'].loc[pat.hicno]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 67,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def score_disp(a):\n",
    "    if a == '[]':\n",
    "        b='0'\n",
    "    else:\n",
    "        b=a[2:][:-3]\n",
    "    return b\n",
    "\n",
    "score_com=[]\n",
    "for pat in cohort_patients:\n",
    "    score_com.append(score_disp(str(score(pat,\"community\",Score).data)))\n",
    "patients['score_com']=score_com"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 68,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style>\n",
       "    .dataframe thead tr:only-child th {\n",
       "        text-align: right;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: left;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>hicno</th>\n",
       "      <th>sex</th>\n",
       "      <th>DOB</th>\n",
       "      <th>MCAID</th>\n",
       "      <th>NEMCAID</th>\n",
       "      <th>F0_34</th>\n",
       "      <th>F0_34_data</th>\n",
       "      <th>F35_44</th>\n",
       "      <th>F35_44_data</th>\n",
       "      <th>F45_54</th>\n",
       "      <th>...</th>\n",
       "      <th>HCC173_data</th>\n",
       "      <th>HCC176</th>\n",
       "      <th>HCC176_data</th>\n",
       "      <th>HCC186</th>\n",
       "      <th>HCC186_data</th>\n",
       "      <th>HCC188</th>\n",
       "      <th>HCC188_data</th>\n",
       "      <th>HCC189</th>\n",
       "      <th>HCC189_data</th>\n",
       "      <th>score_com</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6348</td>\n",
       "      <td>female</td>\n",
       "      <td>1952-12-19 00:00:00</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.213</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>75644</td>\n",
       "      <td>female</td>\n",
       "      <td>1956-05-16 00:00:00</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.416</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>97652</td>\n",
       "      <td>female</td>\n",
       "      <td>1948-06-30 00:00:00</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.74</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>345678</td>\n",
       "      <td>female</td>\n",
       "      <td>1956-12-07 00:00:00</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.416</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>553553</td>\n",
       "      <td>female</td>\n",
       "      <td>1964-01-13 00:00:00</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>1</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.274</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>564416</td>\n",
       "      <td>female</td>\n",
       "      <td>1948-01-10 00:00:00</td>\n",
       "      <td>True</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.45699999999999996</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>576542</td>\n",
       "      <td>female</td>\n",
       "      <td>1956-02-26 00:00:00</td>\n",
       "      <td>False</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.416</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>1515655</td>\n",
       "      <td>female</td>\n",
       "      <td>1959-06-23 00:00:00</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.359</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>3737486</td>\n",
       "      <td>female</td>\n",
       "      <td>1950-02-18 00:00:00</td>\n",
       "      <td>True</td>\n",
       "      <td>True</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.496</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>5444646</td>\n",
       "      <td>female</td>\n",
       "      <td>1946-02-02 00:00:00</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.59</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>5453646</td>\n",
       "      <td>female</td>\n",
       "      <td>1954-06-20 00:00:00</td>\n",
       "      <td>False</td>\n",
       "      <td>False</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0</td>\n",
       "      <td>[]</td>\n",
       "      <td>0.416</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>11 rows × 266 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "      hicno     sex                  DOB  MCAID NEMCAID  F0_34 F0_34_data  \\\n",
       "0      6348  female  1952-12-19 00:00:00   True    True      0         []   \n",
       "1     75644  female  1956-05-16 00:00:00   True   False      0         []   \n",
       "2     97652  female  1948-06-30 00:00:00   True    True      0         []   \n",
       "3    345678  female  1956-12-07 00:00:00   True    True      0         []   \n",
       "4    553553  female  1964-01-13 00:00:00  False   False      0         []   \n",
       "5    564416  female  1948-01-10 00:00:00   True   False      0         []   \n",
       "6    576542  female  1956-02-26 00:00:00  False    True      0         []   \n",
       "7   1515655  female  1959-06-23 00:00:00  False   False      0         []   \n",
       "8   3737486  female  1950-02-18 00:00:00   True    True      0         []   \n",
       "9   5444646  female  1946-02-02 00:00:00  False   False      0         []   \n",
       "10  5453646  female  1954-06-20 00:00:00  False   False      0         []   \n",
       "\n",
       "    F35_44 F35_44_data  F45_54         ...          HCC173_data  HCC176  \\\n",
       "0        0          []       0         ...                   []       0   \n",
       "1        0          []       0         ...                   []       0   \n",
       "2        0          []       0         ...                   []       0   \n",
       "3        0          []       0         ...                   []       0   \n",
       "4        0          []       1         ...                   []       0   \n",
       "5        0          []       0         ...                   []       0   \n",
       "6        0          []       0         ...                   []       0   \n",
       "7        0          []       0         ...                   []       0   \n",
       "8        0          []       0         ...                   []       0   \n",
       "9        0          []       0         ...                   []       0   \n",
       "10       0          []       0         ...                   []       0   \n",
       "\n",
       "   HCC176_data  HCC186 HCC186_data  HCC188 HCC188_data  HCC189 HCC189_data  \\\n",
       "0           []       0          []       0          []       0          []   \n",
       "1           []       0          []       0          []       0          []   \n",
       "2           []       0          []       0          []       0          []   \n",
       "3           []       0          []       0          []       0          []   \n",
       "4           []       0          []       0          []       0          []   \n",
       "5           []       0          []       0          []       0          []   \n",
       "6           []       0          []       0          []       0          []   \n",
       "7           []       0          []       0          []       0          []   \n",
       "8           []       0          []       0          []       0          []   \n",
       "9           []       0          []       0          []       0          []   \n",
       "10          []       0          []       0          []       0          []   \n",
       "\n",
       "              score_com  \n",
       "0                 0.213  \n",
       "1                 0.416  \n",
       "2                  0.74  \n",
       "3                 0.416  \n",
       "4                 0.274  \n",
       "5   0.45699999999999996  \n",
       "6                 0.416  \n",
       "7                 0.359  \n",
       "8                 0.496  \n",
       "9                  0.59  \n",
       "10                0.416  \n",
       "\n",
       "[11 rows x 266 columns]"
      ]
     },
     "execution_count": 68,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "patients"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "patients.to_excel('Patients.xlsx')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "print((indicator(B,CC) & CC.in_(cvars) & coefficient(\"CE_\"+CC,Coef)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "indicator(B,'OriginallyDisabled_Male').__dict__"
   ]
  }
 ],
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