Changes associated with IDR analysis and updates.

src/main/java/org/mitre/synthea/engine/Distribution.java

@@ -11,7 +11,7 @@
  */
 public class Distribution implements Serializable {
   public enum Kind {
-    EXACT, GAUSSIAN, UNIFORM, EXPONENTIAL
+    EXACT, GAUSSIAN, UNIFORM, EXPONENTIAL, TRIANGULAR
   }
 
   public Kind kind;
@@ -50,8 +50,23 @@ public double generate(Person person) {
         break;
       case EXPONENTIAL:
         double average = this.parameters.get("mean");
-        double lambda = (1.0d / average);
-        value = 1.0d + Math.log(1.0d - person.rand()) / (-1.0d * lambda);
+        double lambda = (-1.0d / average);
+        value = 1.0d + Math.log(1.0d - person.rand()) / lambda;
+        break;
+      case TRIANGULAR:
+        /* Pick a single value based on a triangular distribution. See:
+         * https://en.wikipedia.org/wiki/Triangular_distribution
+         */
+        double min = this.parameters.get("min");
+        double mode = this.parameters.get("mode");
+        double max = this.parameters.get("max");
+        double f = (mode - min) / (max - min);
+        double rand = person.rand();
+        if (rand < f) {
+          value = min + Math.sqrt(rand * (max - min) * (mode - min));
+        } else {
+          value = max - Math.sqrt((1 - rand) * (max - min) * (max - mode));
+        }
         break;
       default:
         value = -1;
@@ -81,6 +96,10 @@ public boolean validate() {
             && this.parameters.containsKey("standardDeviation");
       case EXPONENTIAL:
         return this.parameters.containsKey("mean");
+      case TRIANGULAR:
+        return this.parameters.containsKey("min")
+            && this.parameters.containsKey("mode")
+            && this.parameters.containsKey("max");
       default:
         return false;
     }

src/main/java/org/mitre/synthea/export/CSVExporter.java

@@ -308,14 +308,14 @@ private void writeCSVHeaders() throws IOException {
         "START,STOP,PATIENT,PAYER,ENCOUNTER,CODE,DESCRIPTION,BASE_COST,PAYER_COVERAGE,DISPENSES,"
         + "TOTALCOST,REASONCODE,REASONDESCRIPTION");
     medications.write(NEWLINE);
-    conditions.write("START,STOP,PATIENT,ENCOUNTER,CODE,DESCRIPTION");
+    conditions.write("START,STOP,PATIENT,ENCOUNTER,SYSTEM,CODE,DESCRIPTION");
     conditions.write(NEWLINE);
     careplans.write(
         "Id,START,STOP,PATIENT,ENCOUNTER,CODE,DESCRIPTION,REASONCODE,REASONDESCRIPTION");
     careplans.write(NEWLINE);
     observations.write("DATE,PATIENT,ENCOUNTER,CATEGORY,CODE,DESCRIPTION,VALUE,UNITS,TYPE");
     observations.write(NEWLINE);
-    procedures.write("START,STOP,PATIENT,ENCOUNTER,CODE,DESCRIPTION,BASE_COST,"
+    procedures.write("START,STOP,PATIENT,ENCOUNTER,SYSTEM,CODE,DESCRIPTION,BASE_COST,"
         + "REASONCODE,REASONDESCRIPTION");
     procedures.write(NEWLINE);
     immunizations.write("DATE,PATIENT,ENCOUNTER,CODE,DESCRIPTION,BASE_COST");
@@ -752,7 +752,7 @@ private String encounter(String personID,
    * @throws IOException if any IO error occurs
    */
   private void condition(String personID, String encounterID, Entry condition) throws IOException {
-    // START,STOP,PATIENT,ENCOUNTER,CODE,DESCRIPTION
+    // START,STOP,PATIENT,ENCOUNTER,SYSTEM,CODE,DESCRIPTION
     StringBuilder s = new StringBuilder();
 
     s.append(dateFromTimestamp(condition.start)).append(',');
@@ -765,6 +765,7 @@ private void condition(String personID, String encounterID, Entry condition) thr
 
     Code coding = condition.codes.get(0);
 
+    s.append(coding.system).append(',');
     s.append(coding.code).append(',');
     s.append(clean(coding.display));
 
@@ -903,7 +904,7 @@ private void observation(String personID,
    */
   private void procedure(String personID, String encounterID,
       Procedure procedure) throws IOException {
-    // START,STOP,PATIENT,ENCOUNTER,CODE,DESCRIPTION,COST,REASONCODE,REASONDESCRIPTION
+    // START,STOP,PATIENT,ENCOUNTER,SYSTEM,CODE,DESCRIPTION,COST,REASONCODE,REASONDESCRIPTION
     StringBuilder s = new StringBuilder();
 
     s.append(iso8601Timestamp(procedure.start)).append(',');
@@ -915,6 +916,7 @@ private void procedure(String personID, String encounterID,
     s.append(encounterID).append(',');
     // CODE
     Code coding = procedure.codes.get(0);
+    s.append(coding.system).append(',');
     s.append(coding.code).append(',');
     // DESCRIPTION
     s.append(clean(coding.display)).append(',');

src/main/java/org/mitre/synthea/export/ExportHelper.java

@@ -214,6 +214,9 @@ public static long nextFriday(long time) {
   private static final String CVX_URI = "http://hl7.org/fhir/sid/cvx";
   private static final String DICOM_DCM_URI = "http://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_CID_29.html";
   private static final String CDT_URI = "http://www.ada.org/cdt";
+  private static final String ICD9_URI = "http://hl7.org/fhir/sid/icd-9-cm";
+  private static final String ICD10_URI = "http://hl7.org/fhir/sid/icd-10";
+  private static final String ICD10_CM_URI = "http://hl7.org/fhir/sid/icd-10-cm";
 
   /**
    * Translate the system name (e.g. SNOMED-CT) into the official
@@ -234,6 +237,12 @@ public static String getSystemURI(String system) {
       system = DICOM_DCM_URI;
     } else if (system.equals("CDT")) {
       system = CDT_URI;
+    } else if (system.equals("ICD9")) {
+      system = ICD9_URI;
+    } else if (system.equals("ICD10")) {
+      system = ICD10_URI;
+    } else if (system.equals("ICD10-CM")) {
+      system = ICD10_CM_URI;
     }
     return system;
   }
@@ -258,6 +267,12 @@ public static String getSystemFromURI(String uri) {
         return "DICOM-DCM";
       case CDT_URI:
         return "CDT";
+      case ICD9_URI:
+        return "ICD9";
+      case ICD10_URI:
+        return "ICD10";
+      case ICD10_CM_URI:
+        return "ICD10-CM";
       default:
         return "Unknown";
     }

src/main/java/org/mitre/synthea/export/rif/CodeMapper.java

@@ -263,7 +263,7 @@ public List<? extends Map<String, String>> getMissingCodes() {
       row.put("count", count.toString());
       missingCodeList.add(row);
     });
-    // sort in decending order by count
+    // sort in descending order by count
     Collections.sort(missingCodeList, (o1, o2) -> {
       return (int)(Long.parseLong(o2.get("count")) - Long.parseLong(o1.get("count")));
     });

src/main/java/org/mitre/synthea/export/rif/RIFExporter.java

@@ -188,7 +188,11 @@ protected List<String> getDiagnosesCodes(Person person, long time) {
       if (encounter.start <= time) {
         for (HealthRecord.Entry dx : encounter.conditions) {
           if (dx.start <= time && (dx.stop == 0L || dx.stop > time)) {
-            if (exporter.conditionCodeMapper.canMap(dx.codes.get(0))) {
+            if (dx.codes.get(0).system.startsWith("ICD10")) {
+              // Temporarily duplicate the code... we'll remove it later.
+              dx.codes.add(dx.codes.get(0));
+              diagnoses.add(dx);
+            } else if (exporter.conditionCodeMapper.canMap(dx.codes.get(0))) {
               String mapped = exporter.conditionCodeMapper.map(dx.codes.get(0), person, true);
               // Temporarily add the mapped code... we'll remove it later.
               HealthRecord.Code mappedCode = new HealthRecord.Code("ICD10", mapped,
@@ -234,7 +238,9 @@ protected long getEarliestDiagnosis(Person person, String code) {
     List<HealthRecord.Entry> diagnoses = new ArrayList<HealthRecord.Entry>();
     for (HealthRecord.Encounter encounter : person.record.encounters) {
       for (HealthRecord.Entry dx : encounter.conditions) {
-        if (exporter.conditionCodeMapper.canMap(dx.codes.get(0).code)) {
+        if (dx.codes.get(0).system.startsWith("ICD10")) {
+          diagnoses.add(dx);
+        } else if (exporter.conditionCodeMapper.canMap(dx.codes.get(0).code)) {
           String mapped = exporter.conditionCodeMapper.map(dx.codes.get(0).code, person, true);
           if (mapped.equals(code)) {
             diagnoses.add(dx);

src/main/java/org/mitre/synthea/world/concepts/Costs.java

@@ -6,8 +6,8 @@
 import java.util.List;
 import java.util.Map;
 
+import org.mitre.synthea.engine.Distribution;
 import org.mitre.synthea.helpers.Config;
-import org.mitre.synthea.helpers.RandomNumberGenerator;
 import org.mitre.synthea.helpers.SimpleCSV;
 import org.mitre.synthea.helpers.Utilities;
 import org.mitre.synthea.world.agents.Person;
@@ -16,6 +16,8 @@
 import org.mitre.synthea.world.geography.Location;
 
 public class Costs {
+  private static final Distribution.Kind COST_METHOD = parseCostMethod();
+
   // all of these are CSVs with these columns:
   // code, min cost in $, mode cost in $, max cost in $, comments
   private static final Map<String, CostData> PROCEDURE_COSTS =
@@ -144,7 +146,7 @@ public static double determineCostOfEntry(Entry entry, Person person) {
       return 0.0;
     }
 
-    String code = entry.codes.get(0).code;;
+    String code = entry.codes.get(0).code;
     // Retrieve the base cost based on the code.
     double baseCost;
     if (costs != null && costs.containsKey(code)) {
@@ -256,6 +258,17 @@ private static Map<String, Double> parseEncounterAdjustmentFactors(String resour
     }
   }
 
+  /**
+   * Load the cost methodology.
+   * @return a Distribution.Kind enum value. Defaults to Triangular.
+   */
+  private static Distribution.Kind parseCostMethod() {
+    String configValue =
+        Config.get("generate.costs.method", Distribution.Kind.TRIANGULAR.toString());
+    Distribution.Kind distribution = Distribution.Kind.valueOf(configValue.toUpperCase());
+    return distribution;
+  }
+
   /**
    * Whether or not this HealthRecord.Entry has an associated cost on a claim.
    * Billing cost is not necessarily reimbursed cost or paid cost.
@@ -298,39 +311,64 @@ protected static class CostData {
     private double min;
     private double mode;
     private double max;
+    private Distribution distribution;
 
-    private CostData(double min, double mode, double max) {
+    CostData(double min, double mode, double max) {
       this.min = min;
       this.mode = mode;
       this.max = max;
+      this.distribution = new Distribution();
+      this.distribution.kind = COST_METHOD;
+      this.distribution.round = false;
+      this.distribution.parameters = new HashMap<String, Double>();
+      switch (COST_METHOD) {
+        case EXACT:
+          this.distribution.parameters.put("value", this.mode);
+          break;
+        case UNIFORM:
+          this.distribution.parameters.put("low", this.min);
+          this.distribution.parameters.put("high", this.max);
+          break;
+        case GAUSSIAN:
+          this.distribution.parameters.put("mean", this.mode);
+          this.distribution.parameters.put("min", this.min);
+          this.distribution.parameters.put("max", this.max);
+          double left = (this.mode - this.min) / 4.0d;
+          double right = (this.max - this.mode) / 4.0d;
+          double sd = Math.min(left, right);
+          this.distribution.parameters.put("standardDeviation", sd);
+          break;
+        case EXPONENTIAL:
+          this.distribution.parameters.put("mean", this.mode);
+          break;
+        case TRIANGULAR:
+          this.distribution.parameters.put("min", this.min);
+          this.distribution.parameters.put("mode", this.mode);
+          this.distribution.parameters.put("max", this.max);
+          break;
+        default:
+          break;
+      }
     }
 
     /**
-     * Select an individual cost based on this cost data. Uses a triangular
-     * distribution to pick a randomized value.
-     * @param rand Source of randomness
+     * Select an individual cost based on this cost data.
+     * @param person Source of randomness
      * @return Single cost within the range this set of cost data represents
      */
-    private double chooseCost(RandomNumberGenerator rand) {
-      return triangularDistribution(min, max, mode, rand.rand());
-    }
+    protected double chooseCost(Person person) {
+      double value = this.distribution.generate(person);
 
-    /**
-     * Pick a single value based on a triangular distribution. See:
-     * https://en.wikipedia.org/wiki/Triangular_distribution
-     * @param min  Lower limit of the distribution
-     * @param max  Upper limit of the distribution
-     * @param mode Most common value
-     * @param rand A random value between 0-1
-     * @return a single value from the distribution
-     */
-    public static double triangularDistribution(double min, double max, double mode, double rand) {
-      double f = (mode - min) / (max - min);
-      if (rand < f) {
-        return min + Math.sqrt(rand * (max - min) * (mode - min));
-      } else {
-        return max - Math.sqrt((1 - rand) * (max - min) * (max - mode));
+      if (COST_METHOD.equals(Distribution.Kind.EXPONENTIAL)) {
+        value = value - 1.0;
+      }
+
+      if (value < this.min) {
+        value = this.min;
+      } else if (value > this.max) {
+        value = this.max;
       }
+      return value;
     }
   }
 }

src/main/java/org/mitre/synthea/world/concepts/HealthRecord.java

@@ -98,7 +98,7 @@ public boolean equals(Object obj) {
      *
      * @param system  the URI identifier of the code system
      * @param code    the code itself
-     * @param display human-readable description of the coe
+     * @param display human-readable description of the code
      */
     public Code(String system, String code, String display) {
       this.system = system;