Merge pull request synthetichealth#149 from synthetichealth/diabetes_fixes

Diabetes Validation

Author: jawalonoski

config/synthea.yml

@@ -142,6 +142,7 @@ synthea:
         bs_degree: [0.5, 1.0]
   generic:
     log: false
+    log_state_statistics: false
   version_identifier: <%= `git rev-parse HEAD` %> # get the current git commit hash
   graphviz:
     output: './output/graphviz/'

lib/generic/modules/metabolic_syndrome_care.json

@@ -301,7 +301,7 @@
                 "condition_type" : "Attribute",
                 "attribute" : "diabetes_severity",
                 "operator" : ">=",
-                "value" : 1
+                "value" : 2
               },
               {
                 "condition_type" : "Not",
@@ -346,7 +346,7 @@
                 "condition_type" : "Attribute",
                 "attribute" : "diabetes_severity",
                 "operator" : ">=",
-                "value" : 2
+                "value" : 3
               },
               {
                 "condition_type" : "Not",
@@ -371,7 +371,7 @@
                 "condition_type" : "Attribute",
                 "attribute" : "diabetes_severity",
                 "operator" : "<",
-                "value" : 2
+                "value" : 3
               },
               {
                 "condition_type" : "Active Medication",
@@ -424,7 +424,7 @@
                 "condition_type" : "Attribute",
                 "attribute" : "diabetes_severity",
                 "operator" : ">=",
-                "value" : 3
+                "value" : 4
               },
               {
                 "condition_type" : "Not",
@@ -449,7 +449,7 @@
                 "condition_type" : "Attribute",
                 "attribute" : "diabetes_severity",
                 "operator" : "<",
-                "value" : 3
+                "value" : 4
               },
               {
                 "condition_type" : "Active Medication",
@@ -493,13 +493,20 @@
 
     "Insulin" : {
       "type" : "Simple",
+      "remarks" : ["around a third of patients with type 2 diabetes are on insulin ",
+                   "30.8% (17.8% only insulin and 13.0% insulin and other med)",
+                   "https://www.cdc.gov/diabetes/statistics/meduse/fig2.htm",
+                   "coincidentally around a third of patients have nephropathy",
+                   "for simplicity we'll make this a 1-1 relationship so that nephropathy --> insulin"],
       "conditional_transition" : [
         {
           "condition" : {
-            "condition_type" : "Attribute",
-            "attribute" : "diabetes_severity",
-            "operator" : ">=",
-            "value" : 4
+            "condition_type" : "Active Condition",
+            "codes" : [{
+              "system" : "SNOMED-CT",
+              "code" : "127013003",
+              "display" : "Diabetic renal disease (disorder)"
+            }]
           },
           "transition" : "Prescribe_Insulin"
         },
@@ -1422,18 +1429,29 @@
       "complex_transition" : [
         {
           "condition" : {
-          "condition_type" : "Active Condition",
-          "codes" : [{
-            "system" : "SNOMED-CT",
-            "code" : "368581000119106",
-            "display" : "Neuropathy due to type 2 diabetes mellitus (disorder)"
-          }]
+            "condition_type" : "PriorState",
+            "name" : "Amputation_Necessary",
+            "within" : { "quantity" : 1, "unit" : "years" }
+          },
+          "remarks" : ["dialysis means this check is made every few days which can skew results.",
+                       "we only want to consider amputation once a year"],
+          "transition" : "No_Amputation_Necessary"
+        },
+        {
+          "condition" : {
+            "condition_type" : "Active Condition",
+            "codes" : [{
+              "system" : "SNOMED-CT",
+              "code" : "368581000119106",
+              "display" : "Neuropathy due to type 2 diabetes mellitus (disorder)"
+            }]
           },
           "distributions" : [
             { "distribution" : 0.0025, "transition" : "Amputation_Necessary" },
             { "distribution" : 0.9975, "transition" : "No_Amputation_Necessary" }
           ],
-          "remarks" : ["Amputations resulting from type-2 diabetes in the US occur in 0.25% of the population",
+          "remarks" : ["In 2010, about 73,000 non-traumatic lower-limb amputations were performed in adults aged 20 years or older with diagnosed diabetes.",
+                       "28.9 million adults had diagnosed diabetes. 73,000/ 28,900,000 = 0.0025 or 0.25% per year",
                        "https://www.cdc.gov/diabetes/data/statistics/2014statisticsreport.html"]
         },
         {
@@ -1477,7 +1495,7 @@
 
     "Delay_Before_Amputation" : {
       "type" : "Delay",
-      "exact" : { "quantity" : "6", "unit" : "weeks" },
+      "exact" : { "quantity" : 6, "unit" : "weeks" },
       "direct_transition" : "Amputation"
     },