add mapping for icu admit source, ref #14

MIT-LCP · Dec 13, 2017 · 3702563 · 3702563
1 parent c362869
commit 3702563
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Showing 2 changed files with 54 additions and 4 deletions.
diff --git a/anzics/load-data.ipynb b/anzics/load-data.ipynb
@@ -66,6 +66,17 @@
     "df['data_source'] = 'anzics'"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": false
+   },
+   "outputs": [],
+   "source": [
+    "print([x for x in df.columns])"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -209,15 +220,23 @@
     "    4: 'Unknown'\n",
     "}\n",
     "\n",
+    "# below is the original definition according to ANZICS\n",
     "dict_icuadmit = {\n",
     "    1: 'OT/Recovery',\n",
     "    2: 'Accident & Emergency',\n",
     "    3: 'Ward',\n",
     "    4: 'Other ICU, same Hospital',\n",
     "    5: 'Other Hospital',\n",
     "    6: 'Other Hospital ICU'}\n",
-    "\n",
-    "\n",
+    "# we merge the above fields into a standard set\n",
+    "dict_icuadmit_gossis = {\n",
+    "    1: 'Operating Room / Recovery',\n",
+    "    2: 'Accident & Emergency',\n",
+    "    3: 'Floor', # was: Ward\n",
+    "    4: 'Other ICU', # was: 'Other ICU, same Hospital',\n",
+    "    5: 'Other Hospital',\n",
+    "    6: 'Other ICU' # was: 'Other Hospital ICU'\n",
+    "}\n",
     "apsFcn = lambda x: x['albuminscore'] + x['bilirubinscore'] + x['creatininescore'] + \\\n",
     "x['glucosescore'] + x['haematocritscore'] + x['heartratescore'] + x['meanarterialpressurescore'] + \\\n",
     "x['sodiumscore'] + x['neurologicalscore'] + x['oxygenationscore'] + x['phscore'] + \\\n",
@@ -305,7 +324,7 @@
     ", ['hospital_disch_location', lambda x: x['hosp_outcm'].map(dict_hospoutcome)]\n",
     ", ['hospital_los_days', lambda x: x['hosp_hrs']/24.0]\n",
     ", ['hospital_death', lambda x: x['died_hosp'].map(dict_hospdied)]\n",
-    ", ['icu_admit_source', lambda x: x['icu_srce'].map(dict_icuadmit)]\n",
+    ", ['icu_admit_source', lambda x: x['icu_srce'].map(dict_icuadmit_gossis)]\n",
     ", ['icu_admit_type', None]\n",
     ", ['icu_disch_location', lambda x: x['icu_outcm'].map(dict_icuoutcome)]\n",
     ", ['pre_icu_los_days', lambda x: x['pre_icu_hrs']/24.0]\n",

diff --git a/eicu/sql/data.sql b/eicu/sql/data.sql
@@ -55,7 +55,38 @@ select
       else null end as hospital_death
 
 
-  , pt.unitadmitsource as icu_admit_source
+  , case
+      when pt.unitadmitsource in
+      (
+        , 'Direct Admit'
+        , 'Emergency Department'
+      ) then 'Accident & Emergency'
+      when pt.unitadmitsource in
+      (
+          'Operating Room'
+        , 'Recovery Room'
+        , 'PACU'
+      ) then 'Operating Room / Recovery'
+      when pt.unitadmitsource in
+      (
+          'Acute Care/Floor'
+        , 'Chest Pain Center'
+        , 'Floor'
+        , 'Step-Down Unit (SDU)'
+        , 'Observation'
+        , 'Other'
+      ) then 'Floor'
+      when pt.unitadmitsource in
+      (
+          'ICU'
+        , 'ICU to SDU'
+        , 'Other ICU'
+      ) then 'Other ICU'
+      when pt.unitadmitsource in
+      (
+          'Other Hospital'
+      ) then 'Other Hospital'
+    else null end as icu_admit_source
   --, pt.unittype as icu_stay_type
   , pt.unitdischargelocation as icu_disch_location
   , -(pt.hospitaladmitoffset/60.0/24.0) as pre_icu_los_days