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,