Add vitals and respiratory

ratschlab · Mar 26, 2024 · 6bb39f9 · 6bb39f9
1 parent 1650203
commit 6bb39f9
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Showing 2 changed files with 130 additions and 12 deletions.
diff --git a/inst/extdata/config/concept-dict/respiratory.json b/inst/extdata/config/concept-dict/respiratory.json
@@ -119,6 +119,82 @@
             "picdb": []
         }
     },
+    "spo2": {
+        "unit": ["%", "% Sat."],
+        "min": 50,
+        "max": 100,
+        "description": "oxygen saturation (pulse oximetry)",
+        "category": "respiratory",
+        "sources": {
+          "eicu": [
+            {
+              "table": "vitalperiodic",
+              "val_var": "sao2",
+              "unit_val": "%",
+              "class": "col_itm"
+            }
+          ],
+          "eicu_demo": [
+            {
+              "table": "vitalperiodic",
+              "val_var": "sao2",
+              "unit_val": "%",
+              "class": "col_itm"
+            }
+          ],
+          "mimic": [
+            {
+              "ids": [646, 220277],
+              "table": "chartevents",
+              "sub_var": "itemid"
+            }
+          ],
+          "mimic_demo": [
+            {
+              "ids": [646, 220277],
+              "table": "chartevents",
+              "sub_var": "itemid"
+            }
+          ]
+        }
+      },
+      "sao2": {
+        "unit": ["%", "% Sat."],
+        "min": 50,
+        "max": 100,
+        "description": "oxygen saturation (arterial blood)",
+        "category": "respiratory",
+        "sources": {
+          "eicu": [
+            {
+              "ids": "O2 Sat (%)",
+              "table": "lab",
+              "sub_var": "labname"
+            }
+          ],
+          "eicu_demo": [
+            {
+              "ids": "O2 Sat (%)",
+              "table": "lab",
+              "sub_var": "labname"
+            }
+          ],
+          "mimic": [
+            {
+              "ids": [834, 220227],
+              "table": "chartevents",
+              "sub_var": "itemid"
+            }
+          ],
+          "mimic_demo": [
+            {
+              "ids": [834, 220227],
+              "table": "chartevents",
+              "sub_var": "itemid"
+            }
+          ]
+        }
+    },
     "o2sat": {
         "unit": [
             "%",
@@ -274,10 +350,7 @@
         "sources": {
             "aumc": [
                 {
-                    "ids": [
-                        8874,
-                        12266
-                    ],
+                    "ids": [8873, 8874, 12266],
                     "table": "numericitems",
                     "sub_var": "itemid"
                 }
@@ -287,6 +360,11 @@
                     "table": "vitalperiodic",
                     "val_var": "respiration",
                     "class": "col_itm"
+                },
+                {
+                  "table": "nursecharting",
+                  "ids": "Respiratory Rate",
+                  "sub_var": "nursingchartcelltypevalname"
                 }
             ],
             "eicu_demo": [

diff --git a/inst/extdata/config/concept-dict/vitals.json b/inst/extdata/config/concept-dict/vitals.json
@@ -12,7 +12,7 @@
         "sources": {
             "aumc": [
                 {
-                    "ids": 6643,
+                    "ids": [6643, 6680, 8842],
                     "table": "numericitems",
                     "sub_var": "itemid"
                 }
@@ -22,13 +22,23 @@
                     "table": "vitalperiodic",
                     "val_var": "systemicdiastolic",
                     "class": "col_itm"
+                },
+                {
+                  "table": "vitalaperiodic",
+                  "val_var": "noninvasivediastolic",
+                  "class": "col_itm"
                 }
             ],
             "eicu_demo": [
                 {
                     "table": "vitalperiodic",
                     "val_var": "systemicdiastolic",
                     "class": "col_itm"
+                },
+                {
+                  "table": "vitalaperiodic",
+                  "val_var": "noninvasivediastolic",
+                  "class": "col_itm"
                 }
             ],
             "hirid": [
@@ -275,7 +285,7 @@
         "sources": {
             "aumc": [
                 {
-                    "ids": 6642,
+                    "ids": [6642, 6679, 8843],
                     "table": "numericitems",
                     "sub_var": "itemid"
                 }
@@ -385,7 +395,7 @@
         "sources": {
             "aumc": [
                 {
-                    "ids": 6641,
+                    "ids": [6641, 6678, 8841],
                     "table": "numericitems",
                     "sub_var": "itemid"
                 }
@@ -395,13 +405,23 @@
                     "table": "vitalperiodic",
                     "val_var": "systemicsystolic",
                     "class": "col_itm"
+                },
+                {
+                  "table": "vitalaperiodic",
+                  "val_var": "noninvasivesystolic",
+                  "class": "col_itm"
                 }
             ],
             "eicu_demo": [
                 {
                     "table": "vitalperiodic",
                     "val_var": "systemicsystolic",
                     "class": "col_itm"
+                },
+                {
+                  "table": "vitalaperiodic",
+                  "val_var": "noninvasivesystolic",
+                  "class": "col_itm"
                 }
             ],
             "hirid": [
@@ -484,11 +504,7 @@
         "sources": {
             "aumc": [
                 {
-                    "ids": [
-                        8658,
-                        13952,
-                        16110
-                    ],
+                    "ids": [8658, 8659, 8662, 11889, 13058, 13059, 13060, 13061, 13062, 13063, 13952, 16110],
                     "table": "numericitems",
                     "sub_var": "itemid"
                 }
@@ -497,14 +513,38 @@
                 {
                     "table": "vitalperiodic",
                     "val_var": "temperature",
+                    "unit_val": "C",
                     "class": "col_itm"
+                },
+                {
+                  "table": "nursecharting",
+                  "ids": "Temperature (C)",
+                  "sub_var": "nursingchartcelltypevalname"
+                },
+                {
+                  "table": "nursecharting",
+                  "ids": "Temperature (F)",
+                  "sub_var": "nursingchartcelltypevalname",
+                  "callback": "combine_callbacks(transform_fun(as.numeric), transform_fun(fahr_to_cels))"
                 }
             ],
             "eicu_demo": [
                 {
                     "table": "vitalperiodic",
                     "val_var": "temperature",
+                    "unit_val": "C",
                     "class": "col_itm"
+                },
+                {
+                  "table": "nursecharting",
+                  "ids": "Temperature (C)",
+                  "sub_var": "nursingchartcelltypevalname"
+                },
+                {
+                  "table": "nursecharting",
+                  "ids": "Temperature (F)",
+                  "sub_var": "nursingchartcelltypevalname",
+                  "callback": "combine_callbacks(transform_fun(as.numeric), transform_fun(fahr_to_cels))"
                 }
             ],
             "hirid": [