fix default value of NPI to 1 for product

HopkinsIDD · Jan 10, 2024 · e08bcda · e08bcda
1 parent 47aec71
commit e08bcda
Show file tree

Hide file tree

Showing 3 changed files with 22 additions and 10 deletions.
diff --git a/flepimop/gempyor_pkg/src/gempyor/NPI/MultiPeriodModifier.py b/flepimop/gempyor_pkg/src/gempyor/NPI/MultiPeriodModifier.py
@@ -34,8 +34,15 @@ def __init__(
         self.pnames_overlap_operation_sum = pnames_overlap_operation_sum
         self.pnames_overlap_operation_reductionprod = pnames_overlap_operation_reductionprod
 
+        self.param_name = npi_config["parameter"].as_str().lower()
+
+        # Value when the NPI is not active. 
+        default_value = 1.0
+        if self.param_name in self.pnames_overlap_operation_sum or self.param_name in self.pnames_overlap_operation_reductionprod:
+            default_value=0.0
+
         self.npi = pd.DataFrame(
-            0.0,
+            default_value,
             index=self.subpops,
             columns=pd.date_range(self.start_date, self.end_date),
         )
@@ -46,12 +53,12 @@ def __init__(
                 "parameter": [""] * len(self.subpops),
                 "start_date": [[self.start_date]] * len(self.subpops),
                 "end_date": [[self.end_date]] * len(self.subpops),
-                "reduction": [0.0] * len(self.subpops),
+                "reduction": [default_value] * len(self.subpops),
             },
             index=self.subpops,
         )
 
-        self.param_name = npi_config["parameter"].as_str().lower()
+
 
         if (loaded_df is not None) and self.name in loaded_df["npi_name"].values:
             self.__createFromDf(loaded_df, npi_config)
@@ -113,8 +120,8 @@ def __checkErrors(self):
         ###     raise ValueError(f"Invalid parameter name: {self.param_name}. Must be one of {REDUCE_PARAMS}")
 
         # Validate
-        if (self.npi == 0).all(axis=None):
-            print(f"Warning: The intervention in config: {self.name} does nothing.")
+        #if (self.npi == 0).all(axis=None):
+        #    print(f"Warning: The intervention in config: {self.name} does nothing.")
 
         # if (self.npi > 1).any(axis=None):
         #     raise ValueError(

diff --git a/flepimop/gempyor_pkg/src/gempyor/NPI/SinglePeriodModifier.py b/flepimop/gempyor_pkg/src/gempyor/NPI/SinglePeriodModifier.py
@@ -33,13 +33,20 @@ def __init__(
 
         self.subpops = subpops
 
+        # Get name of the parameter to reduce
+        self.param_name = npi_config["parameter"].as_str().lower().replace(" ", "")
+
+        default_value = 1.0
+        if self.param_name in self.pnames_overlap_operation_sum or self.param_name in self.pnames_overlap_operation_reductionprod:
+            default_value=0.0
+
         self.npi = pd.DataFrame(
-            0.0,
+            default_value,
             index=self.subpops,
             columns=pd.date_range(self.start_date, self.end_date),
         )
         self.parameters = pd.DataFrame(
-            0.0,
+            default_value,
             index=self.subpops,
             columns=["npi_name", "start_date", "end_date", "parameter", "reduction"],
         )
@@ -99,8 +106,6 @@ def __checkErrors(self):
         #      )
 
     def __createFromConfig(self, npi_config):
-        # Get name of the parameter to reduce
-        self.param_name = npi_config["parameter"].as_str().lower().replace(" ", "")
 
         # Optional config field "subpop"
         # If values of "subpop" is "all" or unspecified, run on all subpops.
@@ -138,7 +143,6 @@ def __createFromDf(self, loaded_df, npi_config):
         self.affected_subpops = set(self.subpops)
         if npi_config["subpop"].exists() and npi_config["subpop"].get() != "all":
             self.affected_subpops = {str(n.get()) for n in npi_config["subpop"]}
-        self.param_name = npi_config["parameter"].as_str().lower().replace(" ", "")
 
         self.parameters = self.parameters[self.parameters.index.isin(self.affected_subpops)]
         self.parameters["npi_name"] = self.name

diff --git a/flepimop/gempyor_pkg/src/gempyor/NPI/StackedModifier.py b/flepimop/gempyor_pkg/src/gempyor/NPI/StackedModifier.py
@@ -79,6 +79,7 @@ def __init__(
                         self.reductions[new_p] = 1
 
             for param in self.param_name:
+
                 # Get reduction return a neutral value for this overlap operation if no parameeter exists
                 reduction = sub_npi.getReduction(param)
                 if param in pnames_overlap_operation_sum:  # re.match("^transition_rate [1234567890]+$",param):