Other-Cause Mortality

The IHME databases supply all-cause mortality, but Dismod-AT uses other-cause mortality. It can impute what it needs to know using all-cause mortality, but it is helpful to add other-cause mortality not just as input data but as a constraint to the model.

We use total mortality as other-cause mortality. The correct formulae to use are for “cause-deleted lifetables” or “cause deletion.”

Omega Constraint

This constrains other-cause mortality using data from mtother, which is the integrand for other-cause mortality.

The choice to use an omega constraint is set in EpiViz-AT, and this is obeyed. If the user does choose to constrain omega, then it is included with the following function.

cascade_at.inputs.utilities.data.calculate_omega(asdr, csmr)

Calculates other cause mortality (omega) from ASDR (mtall – all-cause mortality) and CSMR (mtspecific – cause-specific mortality). For most diseases, mtall is a good approximation to omega, but we calculate omega = mtall - mtspecific in case it isn’t. For diseases without CSMR (self.csmr_cause_id = None), then omega = mtall.

Parameters

• asdr (DataFrame) – data frame with age-specific all-cause mortality rates

• csmr (DataFrame) – data frame with age-specific cause-specific mortality rates

Return type

DataFrame