NANs Quidel

Author: dshemetov

quidel/delphi_quidel/data_tools.py

@@ -302,7 +302,9 @@ def raw_tests_per_device(devices, tests, min_obs):
     se = np.repeat(np.nan, len(devices))
     sample_size = tests
 
-    return tests_per_device, se, sample_size
+    missing_stat = tests
+
+    return tests_per_device, se, sample_size, missing_stat, missing_se, missing_sample_size
 
 def smoothed_tests_per_device(devices, tests, min_obs, max_borrow_obs, pool_days,
                               parent_devices=None, parent_tests=None):

quidel/delphi_quidel/run.py

@@ -12,7 +12,8 @@
 from delphi_utils import (
     add_prefix,
     create_export_csv,
-    get_structured_logger
+    get_structured_logger,
+    NAN_CODES
 )
 
 from .constants import (END_FROM_TODAY_MINUS, EXPORT_DAY_RANGE,
@@ -83,6 +84,13 @@ def run_module(params: Dict[str, Any]):
         test_type = "covid_ag" if "covid_ag" in sensor else "flu_ag"
         print("state", sensor)
         data = dfs[test_type].copy()
+        breakpoint()
+
+        # Default missingness values
+        data["missing_val"] = NAN_CODE["Not Missing"]
+        data["missing_se"] = NAN_CODE["Not Missing"]
+        data["missing_sample_size"] = NAN_CODE["Not Missing"]
+
         state_groups = geo_map("state", data, map_df).groupby("state_id")
         first_date, last_date = data["timestamp"].min(), data["timestamp"].max()