feat: handle additional doses from a data row (#374)

Map ADDL and II columns, in the CSV, to repeat doses in the model
and simulations.

Author: eatyourgreens

pkpdapp/pkpdapp/models/dataset.py

@@ -164,6 +164,12 @@ def replace_data(self, data: pd.DataFrame):
             observation_name = row["OBSERVATION_NAME"]
             route = row['ROUTE']
             infusion_time = row['INFUSION_TIME']
+            try:
+                repeats = int(row['ADDITIONAL_DOSES']) + 1
+                repeat_interval = float(row['INTERDOSE_INTERVAL'])
+            except ValueError:
+                repeats = 1
+                repeat_interval = 1.0
 
             amount_unit = Unit.objects.get(symbol=amount_unit)
 
@@ -201,6 +207,8 @@ def replace_data(self, data: pd.DataFrame):
                     amount=amount,
                     duration=infusion_time,
                     protocol=protocol,
+                    repeats=repeats,
+                    repeat_interval=repeat_interval,
                 )
 
             # insert covariate columns as categorical for now

pkpdapp/pkpdapp/utils/data_parser.py

@@ -61,6 +61,12 @@ class DataParser:
         ],
         "GROUP_ID": [
             "Group ID", "Group", "GROUP", "cohort", "Cohort", "COHORT"
+        ],
+        "ADDITIONAL_DOSES": [
+            "ADDL", "Addl", "addl", "ADDITIONAL_DOSES"
+        ],
+        "INTERDOSE_INTERVAL": [
+            "II", "INFUSION_INTERVAL"
         ]
     }
 
@@ -81,7 +87,9 @@ class DataParser:
         "COMPOUND",
         "ROUTE",
         "INFUSION_TIME",
-        "GROUP_ID"
+        "GROUP_ID",
+        "ADDITIONAL_DOSES",
+        "INTERDOSE_INTERVAL"
     ]
 
     alternate_unit_names = {
@@ -189,6 +197,12 @@ def map_unit_names(x):
         if "GROUP_ID" not in found_cols:
             data["GROUP_ID"] = 1
 
+        # put in default additional dosing columns if not present
+        if "ADDITIONAL_DOSES" not in found_cols:
+            data["ADDITIONAL_DOSES"] = ""
+        if "INTERDOSE_INTERVAL" not in found_cols:
+            data["INTERDOSE_INTERVAL"] = ""
+
         # put in default units if not present, convert any percentage units
         # to dimensionless
         for unit_col in ["TIME_UNIT", "AMOUNT_UNIT", "OBSERVATION_UNIT"]: