Add hhs and nation

Author: chinandrew

doctor_visits/delphi_doctor_visits/geo_maps.py

@@ -64,6 +64,40 @@ def county_to_state(self, data):
 
         return data.groupby("state_id"), "state_id"
 
+    def county_to_hhs(self, data):
+        """Aggregate county data to the HHS region resolution.
+
+        Args:
+            data: dataframe aggregated to the daily-county resolution (all 7 cols expected)
+
+        Returns: tuple of dataframe at the daily-HHS resolution, and geo_id column name
+        """
+        data = self.gmpr.add_geocode(data,
+                                     "fips",
+                                     "hhs",
+                                     from_col="PatCountyFIPS")
+        data.drop(columns="PatCountyFIPS", inplace=True)
+        data = data.groupby(["ServiceDate", "state_id"]).sum().reset_index()
+
+        return data.groupby("hhs"), "hhs"
+
+    def county_to_nation(self, data):
+        """Aggregate county data to the nation resolution.
+
+        Args:
+            data: dataframe aggregated to the daily-county resolution (all 7 cols expected)
+
+        Returns: tuple of dataframe at the daily-nation resolution, and geo_id column name
+        """
+        data = self.gmpr.add_geocode(data,
+                                     "fips",
+                                     "nation",
+                                     from_col="PatCountyFIPS")
+        data.drop(columns="PatCountyFIPS", inplace=True)
+        data = data.groupby(["ServiceDate", "nation"]).sum().reset_index()
+
+        return data.groupby("nation"), "nation"
+
     def county_to_hrr(self, data):
         """Aggregate county data to the HRR resolution.
 

doctor_visits/delphi_doctor_visits/run.py

@@ -48,7 +48,7 @@ def run_module():
     logging.info(f"n_waiting_days:\t{n_waiting_days}")
 
     ## geographies
-    geos = ["state", "msa", "hrr", "county"]
+    geos = ["state", "msa", "hrr", "county", "hhs", "nation"]
 
     ## print out other vars
     logging.info("outpath:\t\t%s", params["export_dir"])

doctor_visits/delphi_doctor_visits/update_sensor.py

@@ -89,7 +89,7 @@ def update_sensor(
       startdate: first sensor date (YYYY-mm-dd)
       enddate: last sensor date (YYYY-mm-dd)
       dropdate: data drop date (YYYY-mm-dd)
-      geo: geographic resolution, one of ["county", "state", "msa", "hrr"]
+      geo: geographic resolution, one of ["county", "state", "msa", "hrr", "nation", "hhs"]
       parallel: boolean to run the sensor update in parallel
       weekday: boolean to adjust for weekday effects
       se: boolean to write out standard errors, if true, use an obfuscated name
@@ -154,8 +154,14 @@ def update_sensor(
         data_groups, _ = geo_map.county_to_msa(data)
     elif geo.lower() == "hrr":
         data_groups, _ = geo_map.county_to_hrr(data)
+    elif geo.lower() == "hhs":
+        data_groups, _ = geo_map.county_to_hhs(data)
+    elif geo.lower() == "nation":
+        data_groups, _ = geo_map.county_to_nation(data)
     else:
-        logging.error(f"{geo} is invalid, pick one of 'county', 'state', 'msa', 'hrr'")
+        logging.error(
+            f"{geo} is invalid, pick one of 'county', 'state', 'msa', 'hrr', 'hhs', 'nation'"
+        )
         return False
     unique_geo_ids = list(data_groups.groups.keys())