Merge pull request #935 from cmu-delphi/hhs-geo

Add hhs and nation to DV

Author: krivard

doctor_visits/delphi_doctor_visits/geo_maps.py

@@ -7,6 +7,7 @@
 Created: 2020-04-18
 Last modified: 2020-04-30 by Aaron Rumack (add megacounty code)
 """
+from functools import partial
 
 import pandas as pd
 from delphi_utils.geomap import GeoMapper
@@ -20,6 +21,14 @@ class GeoMaps:
     def __init__(self):
         """Create the underlying GeoMapper."""
         self.gmpr = GeoMapper()
+        self.geo_func = {"county": partial(self.county_to_megacounty,
+                                           threshold_visits=Config.MIN_RECENT_VISITS,
+                                           threshold_len=Config.RECENT_LENGTH),
+                         "state": self.county_to_state,
+                         "msa": self.county_to_msa,
+                         "hrr": self.county_to_hrr,
+                         "hhs": self.county_to_hhs,
+                         "nation": self.county_to_nation}
 
     @staticmethod
     def convert_fips(x):
@@ -61,6 +70,40 @@ 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", "hhs"]).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

@@ -68,7 +68,7 @@ def run_module(params):
     logging.info("n_waiting_days:\t{n_waiting_days}")
 
     ## geographies
-    geos = ["state", "msa", "hrr", "county"]
+    geos = ["state", "msa", "hrr", "county", "hhs", "nation"]
 
 
     ## print out other vars

doctor_visits/delphi_doctor_visits/update_sensor.py

@@ -78,7 +78,7 @@ 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
@@ -132,19 +132,8 @@ def update_sensor(
 
     # get right geography
     geo_map = GeoMaps()
-    if geo.lower() == "county":
-        data_groups, _ = geo_map.county_to_megacounty(
-            data, Config.MIN_RECENT_VISITS, Config.RECENT_LENGTH
-        )
-    elif geo.lower() == "state":
-        data_groups, _ = geo_map.county_to_state(data)
-    elif geo.lower() == "msa":
-        data_groups, _ = geo_map.county_to_msa(data)
-    elif geo.lower() == "hrr":
-        data_groups, _ = geo_map.county_to_hrr(data)
-    else:
-        logging.error(f"{geo} is invalid, pick one of 'county', 'state', 'msa', 'hrr'")
-        return {}
+    mapping_func = geo_map.geo_func[geo.lower()]
+    data_groups, _ = mapping_func(data)
     unique_geo_ids = list(data_groups.groups.keys())
 
     # run sensor fitting code (maybe in parallel)