Mortality rate.
"""
forecast_mot_path = FBDPath(
f"{gbd_round_id}/future/death/{forecast_mortality_version}")
forecast_mot = open_xr(forecast_mot_path / "_all.nc").data
past_mot_path = FBDPath(
f"{gbd_round_id}/past/death/{past_mortality_version}")
past_mot_file = past_mot_path / "_all.nc"
past_mot = open_xr(past_mot_file).data
past_mot = past_mot.drop("acause")
forecast_mot = concat_past_future(past_mot, forecast_mot, draws, years)
return forecast_mot
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument("--input-version",
type=str,
required=True,
help="Version of input future mortaltiy or ASFR.")
parser.add_argument("--forecast-pop-version",
type=str,
required=True,
help="Version of input future population")
parser.add_argument("--output-version",
type=str,
required=True,
help="Version of outputs")
parser.add_argument("--gbd-round-id",
type=int,
default=5,
sex=sex_id,
years=years_str,
version=version,
exec_file=execf_,
draws=draws,
python=settings.PYTHON_EXEC,
sdi_interaction=sdi_interaction,
oos=oos_arg,
subnat=subnat_arg,
dryrun=dryrun_arg)
print(qsub)
os.popen(qsub)
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description='Run last year constant model')
parser.add_arg_years()
parser.add_arg_draws()
parser.add_arg_dryrun()
parser.add_argument('--version',
type=str,
required=True,
help='run name/version id')
parser.add_argument('--oos',
action='store_true',
help='Whether to run with out-of-sample inputs')
parser.add_argument('--subnational',
action='store_true',
help=('Whether or not to run including the 93 '
'subnational locations used for CSU'))
args = parser.parse_args()
calculated_paf_dir.mkdir(parents=True, exist_ok=True)
directly_modeled_paf_file = (
FBDPath(
gbd_round_id=gbd_round_id,
past_or_future=p_or_f,
stage="paf",
version=directly_modeled_paf)
/ "risk_acause_specific" / f"{acause}_{rei}.nc")
symlink_file_to_directory(
directly_modeled_paf_file, calculated_paf_dir)
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Calculate cause-risk PAFs")
parser.add_argument("--acause", type=str, required=True,
help="Analytical cause")
parser.add_argument("--rei", type=str, required=True, help="Risk")
parser.add_argument("--version", type=str, required=True,
help="String denoting file directory. Ex: 20171212_ha")
parser.add_argument('--directly-modeled-paf', type=str,
help=('Version of directly-modeled PAFs to copy over.'
'Note that currently the code expects the '
'future and past versions to have the same '
'name'),
required=True)
parser.add_argument('--sev', type=str,
help='sev upstream version, in /future/sev/',
required=True)
parser.add_argument('--rrmax', type=str,
to_csv(tfr_fbd_path / "tfr_upper.csv", index=False)
tfr_agg.mean("draw").to_dataframe().reset_index().\
to_csv(tfr_fbd_path / "tfr_agg_based_on_preliminary_pop_mean.csv",
index=False)
tfr_agg_quantiles = tfr_agg.quantile([0.025, 0.975], "draw")
tfr_agg_quantiles.sel(quantile=0.025).to_dataframe().reset_index().\
to_csv(tfr_fbd_path / "tfr_agg_based_on_preliminary_pop_lower.csv",
index=False)
tfr_agg_quantiles.sel(quantile=0.975).to_dataframe().reset_index().\
to_csv(tfr_fbd_path / "tfr_agg_based_on_preliminary_pop_upper.csv",
index=False)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="make asfr_agg, tfr, tfr_agg")
parser.add_argument("--asfr-version",
required=True,
help="Version of the loc-specific asfrs to collect.")
parser.add_argument("--pop-version",
type=str,
required=True,
help="needed for aggregation")
parser.add_argument("--gbd-round-id",
type=int,
required=True,
help="GBD round id")
parser.add_argument("--model",
required=True,
type=str,
help="algo for intercept-shift")
# If past PAF exists, we don't need to recalculate.
if not os.path.exists(outpath_paf_past):
version = 'past'
df_paf = calculate_paf(risk, acause, version, date, years)
save_paf(risk, acause, df_paf, version, date)
version = 'forecast'
df_paf = calculate_paf(risk, acause, version, date, years)
save_paf(risk, acause, df_paf, version, date)
else:
logger.error('No {risk} available for {acause}'.format(
risk=risk, acause=acause))
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Calculate PAFS")
parser.add_argument("--acause",
type=str,
required=True,
help="It's `A Cause', get it?")
parser.add_argument("--date",
type=str,
required=True,
help="String denoting file directory. Ex: 2015_03_21")
parser.add_arg_years()
parser.add_arg_draws()
args = parser.parse_args()
logging.basicConfig(level=logging.INFO)
logger.debug("arguments {}".format(args))
LOGGER.debug("Checking data value for {} scalar".format(acause))
data_value_check(scalar) # make sure no NaNs or <0 in dataarray
save_xr(scalar,
outpath_scalar,
metric="number",
space="identity",
acause=acause,
version=version,
gbd_round_id=gbd_round_id,
no_update_past=str(no_update_past))
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Calculate Scalars")
parser.add_argument("--acause",
type=str,
required=True,
help="Analytical cause")
parser.add_argument("--version",
type=str,
required=True,
help="Version of the upstream PAF FBDPath")
parser.add_argument("--gbd-round-id", type=int, required=True)
parser.add_arg_years(required=True) # for run_scalars.run_script()
parser.add_argument('--no-update-past',
help=('Whether to not update past values. '
'By default we always update past values.'),
action='store_true',
required=False,