Notes on declaring CAUSES_OF_DEATH and CAUSES_OF_DISABILITY

Background

Each disease module can cause two main outcomes - death and disability.

In order to calibrate the overall model's output of deaths and disability with external sources (in particular, GBD studies) we need to: (i) identify where modules are generating deaths or disability that should be combined; (ii) identify where a cause contributes to disability and death; (iii) identify which causes of death/disability in the GBD dataset correspond to the causes that are being represented in a disease module.

This will enable us to:

• Produce summaries of death/disability generated by the model that are internally-consistent and comparable with the GBD datasets;
• Automatically adjust the 'OtherDeathPoll' (which represents deaths from causes other those represented by the disease modules included in a simulation).

Whilst we need to enforce this kind of coherence between disease modules, it remains acceptable (desirable, in fact!) for different disease modules to represent the effects with differing degrees of granularity.

### Approach The causes of death and disability used in each module remains unchanged. But, now, each module must "explain" what is meant by these cause and additional checking is done to prevent/manage conflicts. This is a bit complicated because:

• Some modules are responsible for many different causes of death whilst others are responsible for only one.
• In some cases, two modules are responsible for the same cause.
• The mapping between the causes defined in the module and causes in the GBD is "many-to-many": i.e. some causes of death in the model map to many different causes in the GBD dataset (e.g. 'OtherCancerDeath' --> many different specific causes of cancer in GBD); whilst in other modules many different causes of death are defined which map to a single cause in the GBD data (e.g. a lot of different outcomes in pregnancy map --> 'Maternal Outcomes' in the GBD data).
• The relationship between causes of death and causes of disability

In some cases, this complexity can probably be resolved by authors of disease modules (e.g. sometimes different names given to disabilities or causes of death, without a good reason) and this should be resolved where possible. But, in most cases, we have to find a solution.

Therefore, we must define:

Syntax

Usage

As before, the deaths (by the cause provided by the module) and disability (by the cause provided by the module) are found in the logged output as follows:

• Deaths: ['tlo.methods.demography']['deaths'] : each row is a death, and the column 'cause' is the cause that is passed by the disease module.
• Years Life Lost: [tlo.methods.healtburden]['yll_by_causes_of_death'] : This is a table (by sex, age-group and year) of the years of live lost by the causes of death that are passed by the disease module.
• Years Lived with Disability: [tlo.methods.healtburden]['yld_by_causes_of_disability'] : This is a table (by sex, age-group and year) of the years lived with disability by the causes of disability that is reported by the module in report_daly_values.