From 4d01ab8142ce6c1b241fa302dfc7a7b7e07f529a Mon Sep 17 00:00:00 2001
From: Manuel Burger <manuel.burger@inf.ethz.ch>
Date: Tue, 26 Mar 2024 12:17:10 +0100
Subject: [PATCH] Add `outcome` and `output` configs

---
 inst/extdata/config/concept-dict/outcome.json | 59 ++++++++++++++++++-
 inst/extdata/config/concept-dict/output.json  | 58 +++++++++++++++++-
 2 files changed, 114 insertions(+), 3 deletions(-)

diff --git a/inst/extdata/config/concept-dict/outcome.json b/inst/extdata/config/concept-dict/outcome.json
index af5256f1..c488c703 100644
--- a/inst/extdata/config/concept-dict/outcome.json
+++ b/inst/extdata/config/concept-dict/outcome.json
@@ -215,6 +215,13 @@
           ]
         }
     },
+    "circ_fail": {
+        "description": "circulatory failure",
+        "concepts": ["map", "cf_treat", "lact"],
+        "category": "outcome",
+        "callback": "circ_fail",
+        "class": "rec_cncpt"
+    },
     "dopa60": {
         "concepts": [
             "dopa_rate",
@@ -539,5 +546,55 @@
         ],
         "callback": "susp_inf",
         "class": "rec_cncpt"
-    }
+    },
+    "sep3_abx_cont": {
+        "concepts": ["sofa", "susp_inf_alt"],
+        "description": "sepsis-3 criterion (alt. def.: continuous abx only)",
+        "category": "outcome",
+        "callback": "sep3_abx_cont",
+        "class": "rec_cncpt"
+    },
+    "susp_inf_abx_cont": {
+        "concepts": ["abx_cont", "samp"],
+        "description": "suspected infection (alt. def.: continuous abx only)",
+        "category": "outcome",
+        "aggregate": [
+          [
+            "sum"
+          ],
+          [
+            false
+          ]
+        ],
+        "callback": "susp_inf_abx_cont",
+        "class": "rec_cncpt"
+    },
+    "aki": {
+        "description": "acute kidney injury (KDIGO 1/2/3)",
+        "concepts": "kdigo",
+        "category": "outcome",
+        "callback": "aki",
+        "class": "rec_cncpt"
+      },
+      "kdigo": {
+        "description": "kidney disease improving global outcome staging",
+        "concepts": ["kdigo_crea", "kdigo_urine"],
+        "category": "outcome",
+        "callback": "kdigo",
+        "class": "rec_cncpt"
+      },
+      "kdigo_crea": {
+        "description": "kidney disease improving global outcome creatinine component",
+        "concepts": "crea",
+        "category": "outcome",
+        "callback": "kdigo_crea",
+        "class": "rec_cncpt"
+      },
+      "kdigo_urine": {
+        "description": "kidney disease improving global outcome urine output component",
+        "concepts": ["urine_rate", "weight"],
+        "category": "outcome",
+        "callback": "kdigo_urine",
+        "class": "rec_cncpt"
+      }
 }
\ No newline at end of file
diff --git a/inst/extdata/config/concept-dict/output.json b/inst/extdata/config/concept-dict/output.json
index 73953d48..50659e8d 100644
--- a/inst/extdata/config/concept-dict/output.json
+++ b/inst/extdata/config/concept-dict/output.json
@@ -2,7 +2,7 @@
     "urine": {
         "unit": "mL",
         "min": 0,
-        "max": 2000,
+        "max": 4000,
         "aggregate": "sum",
         "description": "urine output",
         "omopid": 4264378,
@@ -10,7 +10,7 @@
         "sources": {
             "aumc": [
                 {
-                    "ids": 8794,
+                    "ids": [8794, 8796, 8798, 8800, 8803],
                     "table": "numericitems",
                     "sub_var": "itemid"
                 }
@@ -164,6 +164,60 @@
             ]
         }
     },
+    "urine_rate": {
+        "unit": "mL/h",
+        "min": 0,
+        "max": 2000,
+        "aggregate": "max",
+        "description": "urine rate per hour",
+        "category": "output",
+        "sources": {
+          "aumc": [
+            {
+              "class": "fun_itm",
+              "callback": "combine_callbacks(fwd_concept('urine'), urine_rate)"
+            }
+          ],
+          "eicu": [
+            {
+              "class": "fun_itm",
+              "callback": "combine_callbacks(fwd_concept('urine'), urine_rate)"
+            }
+          ],
+          "eicu_demo": [
+            {
+              "class": "fun_itm",
+              "callback": "combine_callbacks(fwd_concept('urine'), urine_rate)"
+            }
+          ],
+          "hirid": [
+            {
+              "ids": 10020000,
+              "table": "observations",
+              "sub_var": "variableid",
+              "class": "hrd_itm"
+            }
+          ],
+          "miiv": [
+            {
+              "class": "fun_itm",
+              "callback": "combine_callbacks(fwd_concept('urine'), urine_rate)"
+            }
+          ],
+          "mimic": [
+            {
+              "class": "fun_itm",
+              "callback": "combine_callbacks(fwd_concept('urine'), urine_rate)"
+            }
+          ],
+          "mimic_demo": [
+            {
+              "class": "fun_itm",
+              "callback": "combine_callbacks(fwd_concept('urine'), urine_rate)"
+            }
+          ]
+        }
+    },
     "urine24": {
         "concepts": "urine",
         "description": "urine output per 24h",