a no-op for now, but allows easy expansion to flu column/signal

Author: melange396

claims_hosp/delphi_claims_hosp/backfill.py

@@ -39,7 +39,8 @@ def store_backfill_file(claims_filepath, _end_date, backfill_dir):
     backfilldata.rename({"ServiceDate": "time_value",
                          "PatCountyFIPS": "fips",
                          "Denominator": "den",
-                         "Covid_like": "num"},
+                         "Covid_like": "num",
+                         "Flu1": "num_flu"},
                         axis=1, inplace=True)
     backfilldata = gmpr.add_geocode(backfilldata, from_code="fips", new_code="state_id",
                            from_col="fips", new_col="state_id")
@@ -49,7 +50,7 @@ def store_backfill_file(claims_filepath, _end_date, backfill_dir):
     else:
         _start_date = _end_date.replace(year=_end_date.year-1)
     selected_columns = ['time_value', 'fips', 'state_id',
-                        'den', 'num']
+                        'den', 'num', 'num_flu']
     backfilldata = backfilldata.loc[(backfilldata["time_value"] >= _start_date)
                                     & (~backfilldata["fips"].isnull()),
                                     selected_columns]

claims_hosp/delphi_claims_hosp/config.py

@@ -13,8 +13,14 @@
 class Config:
     """Static configuration variables."""
 
-    signal_name = "smoothed_covid19_from_claims"
-    signal_weekday_name = "smoothed_adj_covid19_from_claims"
+    signal_name = {
+        "Covid_like": "smoothed_covid19_from_claims",
+        "Flu1": "smoothed_flu_from_claims",
+    }
+    signal_weekday_name = {
+        "Covid_like": "smoothed_adj_covid19_from_claims",
+        "Flu1": "smoothed_adj_flu_from_claims",
+    }
 
     # max number of CPUs available for pool
     MAX_CPU_POOL = 10
@@ -30,7 +36,7 @@ class Config:
     DAY_SHIFT = timedelta(days=0)
 
     # data columns
-    CLAIMS_COUNT_COLS = ["Denominator", "Covid_like"]
+    CLAIMS_COUNT_COLS = ["Denominator", "Covid_like", "Flu1"]
     CLAIMS_DATE_COL = "ServiceDate"
     FIPS_COL = "fips"
     DATE_COL = "timestamp"
@@ -44,6 +50,7 @@ class Config:
         "PatCountyFIPS": str,
         "Denominator": float,
         "Covid_like": float,
+        "Flu1": float,
         "PatAgeGroup": str,
         "Pat HRR ID": str,
     }

claims_hosp/delphi_claims_hosp/load_data.py

@@ -52,7 +52,7 @@ def load_claims_data(claims_filepath, dropdate, base_geo):
 
     return claims_data
 
-def load_data(input_filepath, dropdate, base_geo):
+def load_data(input_filepath, dropdate, base_geo, numerator_name):
     """
     Load in claims data, and combine them.
 
@@ -71,7 +71,7 @@ def load_data(input_filepath, dropdate, base_geo):
 
     # rename numerator and denominator
     data.fillna(0, inplace=True)
-    data["num"] = data["Covid_like"]
+    data["num"] = data[numerator_name]
     data["den"] = data["Denominator"]
     data = data[['num', 'den']]
     data.reset_index(inplace=True)

claims_hosp/delphi_claims_hosp/run.py

@@ -120,30 +120,34 @@ def run_module(params):
             else:
                 logger.info("Starting no weekday adj", geo_type=geo)
 
-            signal_name = Config.signal_weekday_name if weekday else Config.signal_name
-            if params["indicator"]["write_se"]:
-                assert params["indicator"]["obfuscated_prefix"] is not None, \
-                    "supply obfuscated prefix in params.json"
-                signal_name = params["indicator"]["obfuscated_prefix"] + "_" + signal_name
-
-            logger.info("Updating signal name", signal=signal_name)
-            updater = ClaimsHospIndicatorUpdater(
-                startdate,
-                enddate,
-                dropdate,
-                geo,
-                params["indicator"]["parallel"],
-                weekday,
-                params["indicator"]["write_se"],
-                signal_name,
-                logger,
-            )
-            updater.update_indicator(
-                claims_file,
-                params["common"]["export_dir"],
-            )
-            max_dates.append(updater.output_dates[-1])
-            n_csv_export.append(len(updater.output_dates))
+
+            for numerator_name in ["Covid_like"]:#^H^H^H, "Flu1"]:
+
+                signal_name = Config.signal_weekday_name[numerator_name] if weekday else Config.signal_name[numerator_name]
+                if params["indicator"]["write_se"]:
+                    assert params["indicator"]["obfuscated_prefix"] is not None, \
+                        "supply obfuscated prefix in params.json"
+                    signal_name = params["indicator"]["obfuscated_prefix"] + "_" + signal_name
+
+                logger.info("Updating signal name", signal=signal_name)
+                updater = ClaimsHospIndicatorUpdater(
+                    startdate,
+                    enddate,
+                    dropdate,
+                    geo,
+                    params["indicator"]["parallel"],
+                    weekday,
+                    params["indicator"]["write_se"],
+                    signal_name,
+                    numerator_name,
+                    logger,
+                )
+                updater.update_indicator(
+                    claims_file,
+                    params["common"]["export_dir"],
+                )
+                max_dates.append(updater.output_dates[-1])
+                n_csv_export.append(len(updater.output_dates))
         logger.info("Finished updating", geo_type=geo)
 
     # Remove all the raw files

claims_hosp/delphi_claims_hosp/update_indicator.py

@@ -27,7 +27,7 @@ class ClaimsHospIndicatorUpdater:
     # pylint: disable=too-many-instance-attributes, too-many-arguments
     # all variables are used
 
-    def __init__(self, startdate, enddate, dropdate, geo, parallel, weekday, write_se, signal_name, logger):
+    def __init__(self, startdate, enddate, dropdate, geo, parallel, weekday, write_se, signal_name, numerator_name, logger):
         """
         Initialize updater for the claims-based hospitalization indicator.
 
@@ -45,8 +45,8 @@ def __init__(self, startdate, enddate, dropdate, geo, parallel, weekday, write_s
         self.startdate, self.enddate, self.dropdate = [pd.to_datetime(t) for t in
                                                        (startdate, enddate, dropdate)]
 
-        self.geo, self.parallel, self.weekday, self.write_se, self.signal_name = \
-            geo.lower(), parallel, weekday, write_se, signal_name
+        self.geo, self.parallel, self.weekday, self.write_se, self.signal_name, self.numerator_name = \
+            geo.lower(), parallel, weekday, write_se, signal_name, numerator_name
 
         # init in shift_dates, declared here for pylint
         self.burnindate, self.fit_dates, self.burn_in_dates, self.output_dates = \
@@ -147,7 +147,7 @@ def update_indicator(self, input_filepath, outpath):
 
         # load data
         base_geo = Config.HRR_COL if self.geo == Config.HRR_COL else Config.FIPS_COL
-        data = load_data(input_filepath, self.dropdate, base_geo)
+        data = load_data(input_filepath, self.dropdate, base_geo, self.numerator_name)
         data_frame = self.geo_reindex(data)
 
         # handle if we need to adjust by weekday