Untitled.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from redcap import Project\n",
    "import pandas\n",
    "import pandas_profiling\n",
    "p = Project(\"https://cdsweb07.fhcrc.org/redcap/api/index.php?pid=450\", \"BD39A4A247755C00F8BC7EFE72089C35\")\n",
    "form = 'patient_id'\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "('treatment_event', 'graft_rejection', 'vital_status', 'prehct1_treatment', 'response_or_relapse_event', 'gvhd', 'patient_id', 'primary_prophylaxis_against_relapse', 'immunosuppression_kinetics')\n"
     ]
    }
   ],
   "source": [
    "print(p.forms)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "df = p.export_records(forms=[form], format='df')\n",
    "if form != 'vital_status' and form != 'patient_id':\n",
    "    df = df.loc[df['redcap_repeat_instrument'].notnull()]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>redcap_repeat_instrument</th>\n",
       "      <th>redcap_repeat_instance</th>\n",
       "      <th>hct1_dx</th>\n",
       "      <th>al_origin___1</th>\n",
       "      <th>al_origin___2</th>\n",
       "      <th>al_origin___3</th>\n",
       "      <th>hct1_stage___1</th>\n",
       "      <th>hct1_stage___2</th>\n",
       "      <th>hct1_stage___3</th>\n",
       "      <th>hct1_stage___4</th>\n",
       "      <th>...</th>\n",
       "      <th>relapse_mutations___16</th>\n",
       "      <th>relapse_mutations___17</th>\n",
       "      <th>relapse_mutations___18</th>\n",
       "      <th>relapse_mutations___19</th>\n",
       "      <th>relapse_mutations___20</th>\n",
       "      <th>relapse_mutations___21</th>\n",
       "      <th>eln_final_index_relapse</th>\n",
       "      <th>data_entry</th>\n",
       "      <th>data_check</th>\n",
       "      <th>patient_id_complete</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>count</th>\n",
       "      <td>0.0</td>\n",
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       "      <td>345.000000</td>\n",
       "      <td>346.000000</td>\n",
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       "      <td>346.000000</td>\n",
       "      <td>346.000000</td>\n",
       "      <td>346.000000</td>\n",
       "      <td>346.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>346.000000</td>\n",
       "      <td>346.0</td>\n",
       "      <td>346.00000</td>\n",
       "      <td>346.000000</td>\n",
       "      <td>346.00000</td>\n",
       "      <td>346.000000</td>\n",
       "      <td>262.000000</td>\n",
       "      <td>322.000000</td>\n",
       "      <td>240.000000</td>\n",
       "      <td>346.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>mean</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.089855</td>\n",
       "      <td>0.667630</td>\n",
       "      <td>0.280347</td>\n",
       "      <td>0.112717</td>\n",
       "      <td>0.297688</td>\n",
       "      <td>0.115607</td>\n",
       "      <td>0.236994</td>\n",
       "      <td>0.121387</td>\n",
       "      <td>...</td>\n",
       "      <td>0.005780</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00289</td>\n",
       "      <td>0.005780</td>\n",
       "      <td>0.00289</td>\n",
       "      <td>0.005780</td>\n",
       "      <td>3.480916</td>\n",
       "      <td>4.462733</td>\n",
       "      <td>1.004167</td>\n",
       "      <td>1.658960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>std</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.686698</td>\n",
       "      <td>0.471745</td>\n",
       "      <td>0.449819</td>\n",
       "      <td>0.316704</td>\n",
       "      <td>0.457904</td>\n",
       "      <td>0.320216</td>\n",
       "      <td>0.425855</td>\n",
       "      <td>0.327050</td>\n",
       "      <td>...</td>\n",
       "      <td>0.075918</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.05376</td>\n",
       "      <td>0.075918</td>\n",
       "      <td>0.05376</td>\n",
       "      <td>0.075918</td>\n",
       "      <td>1.391552</td>\n",
       "      <td>1.598337</td>\n",
       "      <td>0.064550</td>\n",
       "      <td>0.553663</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>min</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>25%</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.000000</td>\n",
       "      <td>3.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>50%</th>\n",
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       "      <td>NaN</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.000000</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>2.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>75%</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>4.000000</td>\n",
       "      <td>6.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>2.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>max</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>8.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.00000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>1.00000</td>\n",
       "      <td>1.000000</td>\n",
       "      <td>6.000000</td>\n",
       "      <td>11.000000</td>\n",
       "      <td>2.000000</td>\n",
       "      <td>2.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8 rows × 52 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       redcap_repeat_instrument  redcap_repeat_instance     hct1_dx  \\\n",
       "count                       0.0                     0.0  345.000000   \n",
       "mean                        NaN                     NaN    1.089855   \n",
       "std                         NaN                     NaN    0.686698   \n",
       "min                         NaN                     NaN    1.000000   \n",
       "25%                         NaN                     NaN    1.000000   \n",
       "50%                         NaN                     NaN    1.000000   \n",
       "75%                         NaN                     NaN    1.000000   \n",
       "max                         NaN                     NaN    8.000000   \n",
       "\n",
       "       al_origin___1  al_origin___2  al_origin___3  hct1_stage___1  \\\n",
       "count     346.000000     346.000000     346.000000      346.000000   \n",
       "mean        0.667630       0.280347       0.112717        0.297688   \n",
       "std         0.471745       0.449819       0.316704        0.457904   \n",
       "min         0.000000       0.000000       0.000000        0.000000   \n",
       "25%         0.000000       0.000000       0.000000        0.000000   \n",
       "50%         1.000000       0.000000       0.000000        0.000000   \n",
       "75%         1.000000       1.000000       0.000000        1.000000   \n",
       "max         1.000000       1.000000       1.000000        1.000000   \n",
       "\n",
       "       hct1_stage___2  hct1_stage___3  hct1_stage___4         ...           \\\n",
       "count      346.000000      346.000000      346.000000         ...            \n",
       "mean         0.115607        0.236994        0.121387         ...            \n",
       "std          0.320216        0.425855        0.327050         ...            \n",
       "min          0.000000        0.000000        0.000000         ...            \n",
       "25%          0.000000        0.000000        0.000000         ...            \n",
       "50%          0.000000        0.000000        0.000000         ...            \n",
       "75%          0.000000        0.000000        0.000000         ...            \n",
       "max          1.000000        1.000000        1.000000         ...            \n",
       "\n",
       "       relapse_mutations___16  relapse_mutations___17  relapse_mutations___18  \\\n",
       "count              346.000000                   346.0               346.00000   \n",
       "mean                 0.005780                     0.0                 0.00289   \n",
       "std                  0.075918                     0.0                 0.05376   \n",
       "min                  0.000000                     0.0                 0.00000   \n",
       "25%                  0.000000                     0.0                 0.00000   \n",
       "50%                  0.000000                     0.0                 0.00000   \n",
       "75%                  0.000000                     0.0                 0.00000   \n",
       "max                  1.000000                     0.0                 1.00000   \n",
       "\n",
       "       relapse_mutations___19  relapse_mutations___20  relapse_mutations___21  \\\n",
       "count              346.000000               346.00000              346.000000   \n",
       "mean                 0.005780                 0.00289                0.005780   \n",
       "std                  0.075918                 0.05376                0.075918   \n",
       "min                  0.000000                 0.00000                0.000000   \n",
       "25%                  0.000000                 0.00000                0.000000   \n",
       "50%                  0.000000                 0.00000                0.000000   \n",
       "75%                  0.000000                 0.00000                0.000000   \n",
       "max                  1.000000                 1.00000                1.000000   \n",
       "\n",
       "       eln_final_index_relapse  data_entry  data_check  patient_id_complete  \n",
       "count               262.000000  322.000000  240.000000           346.000000  \n",
       "mean                  3.480916    4.462733    1.004167             1.658960  \n",
       "std                   1.391552    1.598337    0.064550             0.553663  \n",
       "min                   1.000000    1.000000    1.000000             0.000000  \n",
       "25%                   3.000000    3.000000    1.000000             1.000000  \n",
       "50%                   3.000000    5.000000    1.000000             2.000000  \n",
       "75%                   4.000000    6.000000    1.000000             2.000000  \n",
       "max                   6.000000   11.000000    2.000000             2.000000  \n",
       "\n",
       "[8 rows x 52 columns]"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.describe()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "ename": "KeyError",
     "evalue": "'vital_status_complete'",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[0;32mC:\\Users\\whiteau\\AppData\\Local\\Continuum\\Anaconda3\\lib\\site-packages\\pandas\\core\\indexes\\base.py\u001b[0m in \u001b[0;36mget_loc\u001b[0;34m(self, key, method, tolerance)\u001b[0m\n\u001b[1;32m   3077\u001b[0m             \u001b[1;32mtry\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3078\u001b[0;31m                 \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_engine\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_loc\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3079\u001b[0m             \u001b[1;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/hashtable_class_helper.pxi\u001b[0m in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/hashtable_class_helper.pxi\u001b[0m in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;31mKeyError\u001b[0m: 'vital_status_complete'",
      "\nDuring handling of the above exception, another exception occurred:\n",
      "\u001b[0;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-24-d580b7bd4c14>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mdf\u001b[0m\u001b[1;33m[\u001b[0m\u001b[1;34m'vital_status_complete'\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32mC:\\Users\\whiteau\\AppData\\Local\\Continuum\\Anaconda3\\lib\\site-packages\\pandas\\core\\frame.py\u001b[0m in \u001b[0;36m__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m   2686\u001b[0m             \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_getitem_multilevel\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   2687\u001b[0m         \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2688\u001b[0;31m             \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_getitem_column\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2689\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   2690\u001b[0m     \u001b[1;32mdef\u001b[0m \u001b[0m_getitem_column\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mC:\\Users\\whiteau\\AppData\\Local\\Continuum\\Anaconda3\\lib\\site-packages\\pandas\\core\\frame.py\u001b[0m in \u001b[0;36m_getitem_column\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m   2693\u001b[0m         \u001b[1;31m# get column\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   2694\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mcolumns\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mis_unique\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2695\u001b[0;31m             \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_get_item_cache\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2696\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   2697\u001b[0m         \u001b[1;31m# duplicate columns & possible reduce dimensionality\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mC:\\Users\\whiteau\\AppData\\Local\\Continuum\\Anaconda3\\lib\\site-packages\\pandas\\core\\generic.py\u001b[0m in \u001b[0;36m_get_item_cache\u001b[0;34m(self, item)\u001b[0m\n\u001b[1;32m   2487\u001b[0m         \u001b[0mres\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mcache\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mitem\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   2488\u001b[0m         \u001b[1;32mif\u001b[0m \u001b[0mres\u001b[0m \u001b[1;32mis\u001b[0m \u001b[1;32mNone\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m-> 2489\u001b[0;31m             \u001b[0mvalues\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_data\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mitem\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   2490\u001b[0m             \u001b[0mres\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_box_item_values\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mitem\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mvalues\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   2491\u001b[0m             \u001b[0mcache\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mitem\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mres\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mC:\\Users\\whiteau\\AppData\\Local\\Continuum\\Anaconda3\\lib\\site-packages\\pandas\\core\\internals.py\u001b[0m in \u001b[0;36mget\u001b[0;34m(self, item, fastpath)\u001b[0m\n\u001b[1;32m   4113\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   4114\u001b[0m             \u001b[1;32mif\u001b[0m \u001b[1;32mnot\u001b[0m \u001b[0misna\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mitem\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m-> 4115\u001b[0;31m                 \u001b[0mloc\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_loc\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mitem\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   4116\u001b[0m             \u001b[1;32melse\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   4117\u001b[0m                 \u001b[0mindexer\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0marange\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0misna\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mitems\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mC:\\Users\\whiteau\\AppData\\Local\\Continuum\\Anaconda3\\lib\\site-packages\\pandas\\core\\indexes\\base.py\u001b[0m in \u001b[0;36mget_loc\u001b[0;34m(self, key, method, tolerance)\u001b[0m\n\u001b[1;32m   3078\u001b[0m                 \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_engine\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_loc\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   3079\u001b[0m             \u001b[1;32mexcept\u001b[0m \u001b[0mKeyError\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m-> 3080\u001b[0;31m                 \u001b[1;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_engine\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_loc\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0m_maybe_cast_indexer\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   3081\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m   3082\u001b[0m         \u001b[0mindexer\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mself\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mget_indexer\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mkey\u001b[0m\u001b[1;33m]\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mmethod\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mmethod\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mtolerance\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mtolerance\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/index.pyx\u001b[0m in \u001b[0;36mpandas._libs.index.IndexEngine.get_loc\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/hashtable_class_helper.pxi\u001b[0m in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;32mpandas/_libs/hashtable_class_helper.pxi\u001b[0m in \u001b[0;36mpandas._libs.hashtable.PyObjectHashTable.get_item\u001b[0;34m()\u001b[0m\n",
      "\u001b[0;31mKeyError\u001b[0m: 'vital_status_complete'"
     ]
    }
   ],
   "source": [
    "df['vital_status_complete']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Empty columns:\n",
      "length, width (346, 10), number of empty columns: 2\n"
     ]
    }
   ],
   "source": [
    "df.isna().sum()\n",
    "length = df.shape[0]\n",
    "print(\"Empty columns:\")\n",
    "num_na = 0\n",
    "empty_cols = [col for col in list(df) if df[col].isna().sum() == length]\n",
    "print(\"length, width {}, number of empty columns: {}\".format(df.shape, len(empty_cols)))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    .dataframe thead th {\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>redcap_repeat_instrument</th>\n",
       "      <th>redcap_repeat_instance</th>\n",
       "      <th>e_status</th>\n",
       "      <th>date_status</th>\n",
       "      <th>w_status_dead</th>\n",
       "      <th>w_status_alive</th>\n",
       "      <th>w_sub_status_notes</th>\n",
       "      <th>days_hct1_to_status</th>\n",
       "      <th>days_index_rel_to_status</th>\n",
       "      <th>vital_status_complete</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>subject_id</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
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       "      <th></th>\n",
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       "  </thead>\n",
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       "      <th>0244017</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2011-09-22</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>Never got off systemic ISP completely because ...</td>\n",
       "      <td>427.0</td>\n",
       "      <td>337.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0277965</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2014-07-29</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1657.0</td>\n",
       "      <td>188.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>0742011</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2016-09-30</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>694.0</td>\n",
       "      <td>632.0</td>\n",
       "      <td>2</td>\n",
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       "    <tr>\n",
       "      <th>1962960</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2017-02-15</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>330.0</td>\n",
       "      <td>153.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2015958</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2014-10-11</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2754.0</td>\n",
       "      <td>1971.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2060522</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>2018-01-18</td>\n",
       "      <td>NaN</td>\n",
       "      <td>2.0</td>\n",
       "      <td>Developing joint and liver cGVHD, on ursodiol....</td>\n",
       "      <td>2261.0</td>\n",
       "      <td>2204.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2097045</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2014-01-19</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>149.0</td>\n",
       "      <td>80.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2114653</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2012-06-13</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>4592.0</td>\n",
       "      <td>694.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2146388</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2010-04-28</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SOS and resp failure and septic shock, with ci...</td>\n",
       "      <td>1533.0</td>\n",
       "      <td>964.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2156305</th>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.0</td>\n",
       "      <td>2005-09-05</td>\n",
       "      <td>1.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1250.0</td>\n",
       "      <td>522.0</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "            redcap_repeat_instrument  redcap_repeat_instance  e_status  \\\n",
       "subject_id                                                               \n",
       "0244017                          NaN                     NaN       1.0   \n",
       "0277965                          NaN                     NaN       1.0   \n",
       "0742011                          NaN                     NaN       1.0   \n",
       "1962960                          NaN                     NaN       1.0   \n",
       "2015958                          NaN                     NaN       1.0   \n",
       "2060522                          NaN                     NaN       2.0   \n",
       "2097045                          NaN                     NaN       1.0   \n",
       "2114653                          NaN                     NaN       1.0   \n",
       "2146388                          NaN                     NaN       1.0   \n",
       "2156305                          NaN                     NaN       1.0   \n",
       "\n",
       "           date_status  w_status_dead  w_status_alive  \\\n",
       "subject_id                                              \n",
       "0244017     2011-09-22            1.0             NaN   \n",
       "0277965     2014-07-29            1.0             NaN   \n",
       "0742011     2016-09-30            1.0             NaN   \n",
       "1962960     2017-02-15            1.0             NaN   \n",
       "2015958     2014-10-11            1.0             NaN   \n",
       "2060522     2018-01-18            NaN             2.0   \n",
       "2097045     2014-01-19            1.0             NaN   \n",
       "2114653     2012-06-13            1.0             NaN   \n",
       "2146388     2010-04-28            1.0             NaN   \n",
       "2156305     2005-09-05            1.0             NaN   \n",
       "\n",
       "                                           w_sub_status_notes  \\\n",
       "subject_id                                                      \n",
       "0244017     Never got off systemic ISP completely because ...   \n",
       "0277965                                                   NaN   \n",
       "0742011                                                   NaN   \n",
       "1962960                                                   NaN   \n",
       "2015958                                                   NaN   \n",
       "2060522     Developing joint and liver cGVHD, on ursodiol....   \n",
       "2097045                                                   NaN   \n",
       "2114653                                                   NaN   \n",
       "2146388     SOS and resp failure and septic shock, with ci...   \n",
       "2156305                                                   NaN   \n",
       "\n",
       "            days_hct1_to_status  days_index_rel_to_status  \\\n",
       "subject_id                                                  \n",
       "0244017                   427.0                     337.0   \n",
       "0277965                  1657.0                     188.0   \n",
       "0742011                   694.0                     632.0   \n",
       "1962960                   330.0                     153.0   \n",
       "2015958                  2754.0                    1971.0   \n",
       "2060522                  2261.0                    2204.0   \n",
       "2097045                   149.0                      80.0   \n",
       "2114653                  4592.0                     694.0   \n",
       "2146388                  1533.0                     964.0   \n",
       "2156305                  1250.0                     522.0   \n",
       "\n",
       "            vital_status_complete  \n",
       "subject_id                         \n",
       "0244017                         2  \n",
       "0277965                         2  \n",
       "0742011                         2  \n",
       "1962960                         2  \n",
       "2015958                         2  \n",
       "2060522                         2  \n",
       "2097045                         2  \n",
       "2114653                         2  \n",
       "2146388                         2  \n",
       "2156305                         2  "
      ]
     },
     "execution_count": 18,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head(10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "\n",
    "\n"
   ]
  }
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