From a4f3dcc78c3d76befa264bb778c549cdbf78793f Mon Sep 17 00:00:00 2001 From: Dmitry Shemetov Date: Wed, 7 Apr 2021 13:37:54 -0700 Subject: [PATCH] NANS doctor visits: * write missing columns * update test files --- .../delphi_doctor_visits/update_sensor.py | 21 +- .../run/20200202_county_smoothed_cli.csv | 4932 +++++++------- .../run/20200202_hhs_smoothed_cli.csv | 11 + .../run/20200202_hrr_smoothed_cli.csv | 614 +- .../run/20200202_msa_smoothed_cli.csv | 768 +-- .../run/20200202_nation_smoothed_cli.csv | 2 + .../run/20200202_state_smoothed_cli.csv | 104 +- .../run/20200203_county_smoothed_cli.csv | 5778 ++++++++-------- .../run/20200203_hhs_smoothed_cli.csv | 11 + .../run/20200203_hrr_smoothed_cli.csv | 614 +- .../run/20200203_msa_smoothed_cli.csv | 770 +-- .../run/20200203_nation_smoothed_cli.csv | 2 + .../run/20200203_state_smoothed_cli.csv | 104 +- .../run/20200204_county_smoothed_cli.csv | 5908 ++++++++--------- .../run/20200204_hhs_smoothed_cli.csv | 11 + .../run/20200204_hrr_smoothed_cli.csv | 614 +- .../run/20200204_msa_smoothed_cli.csv | 770 +-- .../run/20200204_nation_smoothed_cli.csv | 2 + .../run/20200204_state_smoothed_cli.csv | 104 +- .../run/20200205_county_smoothed_cli.csv | 5898 ++++++++-------- .../run/20200205_hhs_smoothed_cli.csv | 11 + .../run/20200205_hrr_smoothed_cli.csv | 614 +- .../run/20200205_msa_smoothed_cli.csv | 770 +-- .../run/20200205_nation_smoothed_cli.csv | 2 + .../run/20200205_state_smoothed_cli.csv | 104 +- 25 files changed, 14303 insertions(+), 14236 deletions(-) create mode 100644 doctor_visits/tests/comparison/run/20200202_hhs_smoothed_cli.csv create mode 100644 doctor_visits/tests/comparison/run/20200202_nation_smoothed_cli.csv create mode 100644 doctor_visits/tests/comparison/run/20200203_hhs_smoothed_cli.csv create mode 100644 doctor_visits/tests/comparison/run/20200203_nation_smoothed_cli.csv create mode 100644 doctor_visits/tests/comparison/run/20200204_hhs_smoothed_cli.csv create mode 100644 doctor_visits/tests/comparison/run/20200204_nation_smoothed_cli.csv create mode 100644 doctor_visits/tests/comparison/run/20200205_hhs_smoothed_cli.csv create mode 100644 doctor_visits/tests/comparison/run/20200205_nation_smoothed_cli.csv 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 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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 -ct,0.175135,NA,NA,NA -dc,0.105202,NA,NA,NA -de,0.113541,NA,NA,NA -fl,0.119330,NA,NA,NA -ga,0.167612,NA,NA,NA -hi,0.123352,NA,NA,NA -ia,0.164783,NA,NA,NA -id,0.113514,NA,NA,NA -il,0.103527,NA,NA,NA -in,0.128793,NA,NA,NA -ks,0.126185,NA,NA,NA -ky,0.111221,NA,NA,NA -la,0.110919,NA,NA,NA -ma,0.156577,NA,NA,NA -md,0.123358,NA,NA,NA -me,0.076956,NA,NA,NA -mi,0.120599,NA,NA,NA -mn,0.173082,NA,NA,NA -mo,0.117793,NA,NA,NA -ms,0.135259,NA,NA,NA -mt,0.106669,NA,NA,NA -nc,0.119628,NA,NA,NA -nd,0.106009,NA,NA,NA -ne,0.152082,NA,NA,NA -nh,0.096743,NA,NA,NA -nj,0.177545,NA,NA,NA -nm,0.109561,NA,NA,NA -nv,0.206484,NA,NA,NA -ny,0.119358,NA,NA,NA -oh,0.138950,NA,NA,NA 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+49660,0.376085,NA,NA,NA,0,3,1 +49700,0.222113,NA,NA,NA,0,3,1 +49740,0.234356,NA,NA,NA,0,3,1 diff --git a/doctor_visits/tests/comparison/run/20200203_nation_smoothed_cli.csv b/doctor_visits/tests/comparison/run/20200203_nation_smoothed_cli.csv new file mode 100644 index 0000000000..ce8b29b3f1 --- /dev/null +++ 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 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b/doctor_visits/tests/comparison/run/20200205_state_smoothed_cli.csv index b29f69e835..6f14e5f64b 100644 --- a/doctor_visits/tests/comparison/run/20200205_state_smoothed_cli.csv +++ b/doctor_visits/tests/comparison/run/20200205_state_smoothed_cli.csv @@ -1,52 +1,52 @@ -geo_id,val,se,direction,sample_size -ak,0.569287,NA,NA,NA -al,0.328228,NA,NA,NA -ar,0.370763,NA,NA,NA -az,0.530073,NA,NA,NA -ca,0.351530,NA,NA,NA -co,0.401868,NA,NA,NA -ct,0.601417,NA,NA,NA -dc,0.878253,NA,NA,NA -de,0.324467,NA,NA,NA -fl,0.479217,NA,NA,NA -ga,0.475930,NA,NA,NA -hi,0.424594,NA,NA,NA -ia,0.481491,NA,NA,NA -id,0.445713,NA,NA,NA -il,0.380958,NA,NA,NA -in,0.357658,NA,NA,NA -ks,0.352002,NA,NA,NA -ky,0.368104,NA,NA,NA -la,0.358186,NA,NA,NA -ma,0.347109,NA,NA,NA -md,0.478480,NA,NA,NA -me,0.292373,NA,NA,NA -mi,0.432469,NA,NA,NA -mn,0.436532,NA,NA,NA -mo,0.354799,NA,NA,NA -ms,0.348631,NA,NA,NA -mt,0.363729,NA,NA,NA -nc,0.502467,NA,NA,NA -nd,0.384162,NA,NA,NA -ne,0.504449,NA,NA,NA -nh,0.406304,NA,NA,NA 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