diff --git a/doctor_visits/delphi_doctor_visits/update_sensor.py b/doctor_visits/delphi_doctor_visits/update_sensor.py index 01e1647fe6..c84809feaf 100644 --- a/doctor_visits/delphi_doctor_visits/update_sensor.py +++ b/doctor_visits/delphi_doctor_visits/update_sensor.py @@ -18,6 +18,7 @@ import pandas as pd # first party +from delphi_utils import Nans from .config import Config from .geo_maps import GeoMaps from .sensor import DoctorVisitsSensor @@ -44,7 +45,10 @@ def write_to_csv(output_df: pd.DataFrame, geo_level, se, out_name, output_path=" out_name) single_date_df = output_df[output_df["date"] == d] with open(filename, "w") as outfile: - outfile.write("geo_id,val,se,direction,sample_size\n") + outfile.write( + "geo_id,val,se,direction,sample_size," + "missing_val,missing_se,missing_sample_size\n" + ) for line in single_date_df.itertuples(): geo_id = line.geo_id @@ -58,11 +62,22 @@ def write_to_csv(output_df: pd.DataFrame, geo_level, se, out_name, output_path=" if se: assert sensor > 0 and se_val > 0, "p=0, std_err=0 invalid" outfile.write( - "%s,%f,%s,%s,%s\n" % (geo_id, sensor, se_val, "NA", "NA")) + "%s,%f,%s,%s,%s,%d,%d,%d\n" % + ( + geo_id, sensor, se, "NA", "NA", + Nans.NOT_MISSING, Nans.NOT_MISSING, Nans.NOT_APPLICABLE + ) + ) else: # for privacy reasons we will not report the standard error outfile.write( - "%s,%f,%s,%s,%s\n" % (geo_id, sensor, "NA", "NA", "NA")) + "%s,%f,%s,%s,%s,%d,%d,%d\n" % + ( + geo_id, sensor, "NA", "NA", "NA", + Nans.NOT_MISSING, Nans.PRIVACY, Nans.NOT_APPLICABLE + ) + ) + out_n += 1 logging.debug(f"wrote {out_n} rows for {geo_level}") diff --git a/doctor_visits/tests/comparison/run/20200202_county_smoothed_cli.csv b/doctor_visits/tests/comparison/run/20200202_county_smoothed_cli.csv index 18857e1f56..8245b31a99 100644 --- a/doctor_visits/tests/comparison/run/20200202_county_smoothed_cli.csv +++ b/doctor_visits/tests/comparison/run/20200202_county_smoothed_cli.csv @@ -1,2466 +1,2466 @@ -geo_id,val,se,direction,sample_size -01001,0.108124,NA,NA,NA -01003,0.769436,NA,NA,NA -01005,0.059130,NA,NA,NA -01007,0.007659,NA,NA,NA -01009,0.054822,NA,NA,NA -01011,0.215876,NA,NA,NA -01013,0.899810,NA,NA,NA -01015,0.153670,NA,NA,NA -01017,0.461089,NA,NA,NA -01019,0.455886,NA,NA,NA -01021,0.373582,NA,NA,NA -01023,0.447206,NA,NA,NA -01025,0.368750,NA,NA,NA -01027,0.295805,NA,NA,NA -01029,0.874569,NA,NA,NA -01031,1.928054,NA,NA,NA -01033,0.216914,NA,NA,NA -01035,0.006460,NA,NA,NA -01037,0.046227,NA,NA,NA -01039,0.329942,NA,NA,NA -01041,0.398341,NA,NA,NA -01043,0.246035,NA,NA,NA -01045,0.315021,NA,NA,NA -01049,0.287304,NA,NA,NA -01051,0.010354,NA,NA,NA -01055,0.229247,NA,NA,NA -01057,0.400859,NA,NA,NA -01059,0.216415,NA,NA,NA -01061,0.014482,NA,NA,NA -01063,0.214192,NA,NA,NA -01065,0.036931,NA,NA,NA -01067,0.643081,NA,NA,NA -01069,0.263671,NA,NA,NA -01071,0.040782,NA,NA,NA -01073,0.121968,NA,NA,NA -01075,0.005900,NA,NA,NA -01077,0.220019,NA,NA,NA -01079,0.076903,NA,NA,NA -01081,0.055511,NA,NA,NA -01083,0.002740,NA,NA,NA 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+49700,0.102610,NA,NA,NA,0,3,1 +49740,0.035005,NA,NA,NA,0,3,1 diff --git a/doctor_visits/tests/comparison/run/20200202_nation_smoothed_cli.csv b/doctor_visits/tests/comparison/run/20200202_nation_smoothed_cli.csv new file mode 100644 index 0000000000..4422f94b95 --- /dev/null +++ b/doctor_visits/tests/comparison/run/20200202_nation_smoothed_cli.csv @@ -0,0 +1,2 @@ +geo_id,val,se,direction,sample_size,missing_val,missing_se,missing_sample_size +us,0.111368,NA,NA,NA,0,3,1 diff --git a/doctor_visits/tests/comparison/run/20200202_state_smoothed_cli.csv b/doctor_visits/tests/comparison/run/20200202_state_smoothed_cli.csv index 6f9951a701..8cf12b51c2 100644 --- a/doctor_visits/tests/comparison/run/20200202_state_smoothed_cli.csv +++ b/doctor_visits/tests/comparison/run/20200202_state_smoothed_cli.csv @@ -1,52 +1,52 @@ -geo_id,val,se,direction,sample_size -ak,0.061831,NA,NA,NA -al,0.108976,NA,NA,NA -ar,0.113245,NA,NA,NA -az,0.184613,NA,NA,NA -ca,0.106941,NA,NA,NA -co,0.123677,NA,NA,NA 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b/doctor_visits/tests/comparison/run/20200203_nation_smoothed_cli.csv @@ -0,0 +1,2 @@ +geo_id,val,se,direction,sample_size,missing_val,missing_se,missing_sample_size +us,0.209653,NA,NA,NA,0,3,1 diff --git a/doctor_visits/tests/comparison/run/20200203_state_smoothed_cli.csv b/doctor_visits/tests/comparison/run/20200203_state_smoothed_cli.csv index ec3411ef97..29a8ed8b9a 100644 --- a/doctor_visits/tests/comparison/run/20200203_state_smoothed_cli.csv +++ b/doctor_visits/tests/comparison/run/20200203_state_smoothed_cli.csv @@ -1,52 +1,52 @@ -geo_id,val,se,direction,sample_size -ak,0.264736,NA,NA,NA -al,0.168138,NA,NA,NA -ar,0.197609,NA,NA,NA -az,0.393111,NA,NA,NA -ca,0.193898,NA,NA,NA -co,0.241673,NA,NA,NA -ct,0.343048,NA,NA,NA -dc,0.945267,NA,NA,NA -de,0.186091,NA,NA,NA -fl,0.261771,NA,NA,NA -ga,0.260490,NA,NA,NA -hi,0.286569,NA,NA,NA -ia,0.288675,NA,NA,NA -id,0.220487,NA,NA,NA -il,0.222882,NA,NA,NA -in,0.237321,NA,NA,NA -ks,0.204396,NA,NA,NA -ky,0.219002,NA,NA,NA -la,0.196611,NA,NA,NA 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